Ionic tags for synthesis of oligoribonucleotides

ABSTRACT

The invention relates to the chemical synthesis of oligonucleotides, e.g., oligoribonucleotides. In another aspect, the invention relates to compounds of formula (II): 
     
       
         
         
             
             
         
       
     
     processes for making these compounds, and the use thereof in the chemical synthesis of oligonucleotides, e.g., oligoribonucleotides. The invention also relates to methods of synthesis of oligomers, including but not limited to oligopeptides, oligosaccharides and oligonucleotides, particularly oligoribonucleotides and also oligodeoxyribonucleotides, in solution systems, and ionic tag linkers for use in methods provided herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of U.S. application Ser.No. 15/925,509 filed Mar. 19, 2018, now issued as U.S. Pat. No.11,014,948; which is a continuation application of U.S. application Ser.No. 14/240,067 filed May 29, 2014, now issued as U.S. Pat. No.9,920,084; which is a 35 USC § 371 National Stage application ofInternational Application No. PCT/CA2012/000784 filed Aug. 23, 2012, nowexpired; which is a continuation-in-part application of InternationalApplication No. PCT/CA2011/000950 filed Aug. 23, 2011, now expired; andclaims the benefit under 35 USC § 119(e) to U.S. Application Ser. No.61/602,373 filed Feb. 23, 2012, now expired. The disclosure of each ofthe prior applications is considered part of and is incorporated byreference in the disclosure of this application.

BACKGROUND OF THE INVENTION Field of the Invention

The invention relates to the chemical synthesis of oligonucleotides, inparticular oligoribonucleotides, in particular solution phase synthesis.

Background Information

The demand for synthetic oligonucleotides has grown exponentially asgenome sequencing, functional genomics, and PCR-based detection methodsconsume enormous quantities of DNA oligonucleotides. In addition, thepotential success of new DNA- and RNA-based therapeutic platforms (suchas antisense and siRNA gene silencing strategies) currently undergoingclinical trials could result in an unprecedented demand for shortsynthetic DNA and RNA molecules.

RNA interference (RNAi) as potential therapeutics represents afundamentally new way to treat human diseases [Manoharan, Curr. Opin.Chem. Biol. 8, 570-579 (2004)]. However, achieving targeted tissue andcellular delivery, stabilization in vivo, and cost effective large scalesynthesis of RNA are significant bottlenecks in the development of RNAitechnology. The reality of mainstream RNAi based therapeutics is rapidlyapproaching and the demand for these compounds on large scale may soonexceed the capability of manufacturers. Therefore, there is a need todevelop synthetic strategies enabling RNA oligomers to be synthesizedrapidly, in high purity and/or in a cost efficient, large scalesynthesis.

Current methods for DNA and RNA synthesis rely on stepwise addition ofmonomeric phosphoramidite units on solid supports [Caruthers, M. H. etal. Methods in Enzymology 154, 287-313 (1987); Alvarado-Urbina, G. etal. Science 214, 270-274 (1981)]. Chain elongation from 3′- to 5′-end ispreferred, which is achieved by coupling of a nucleoside unit having a3′-phosphorus (III) group (in its activated form) to a free 5′-hydroxylgroup of another nucleoside unit. As solid support, 500 to 1000 Åcontrolled pore glass (CPG) support or an organic polymer support, suchas primer polystyrene support PS200, can be used. Chain elongationbegins by cleavage of the 5′-O-dimethoxytrityl group with an organicacid, thus liberating a nucleophilic 5′-hydroxyl group. This terminalnucleophile is then allowed to couple to a protected nucleoside3′-O-phosphoramidite monomer in the presence of an activator. In thecase of RNA synthesis suitable protection of the 2′-hydroxyl group isrequired. Any unreacted 5′-hydroxyl groups are acetylated in a processreferred to as ‘capping’. The most commonly used group used for thispurpose is an acetyl ester. Thus, ‘capping’ with acetic anhydrideesterifies any unreacted 5′-hydroxyl groups and halts the accumulationof by-products. The newly created phosphite triester 3′,5′-linkage isthen oxidized to provide the desired and more stable phosphate triester.This process is repeated until an oligomer of the desired length andsequence is obtained. Cleavage of the oligomer from the solid supportand removal of the protecting groups from the sugars, phosphates andnucleobases provides the desired target oligomer, which is thenseparated from shorter failure sequences by ion exchange high pressureliquid chromatography (HPLC), ion-pair reverse phase HPLC, orpolyacrylamide gel electrophoresis (PAGE). The full length oligomer isthen characterized by mass spectrometry. Meanwhile a large number of DNAoligomers can be synthesized in parallel on DNA microarrays or “genechips” [Ramsay G., Nature Biotechnology 16, 40-44 (1998)].

The same iterative method may be applied toward the synthesis of DNA andRNA oligonucleotides in solution, for example as described recently byDonga et al. using ionic soluble supports [e.g., Donga, R. A. et al., J.Org. Chem. 71, 7907-7910 (2006); Donga, R. A. et al., Can. J. Chem. 85,274-282 (2007)]. The use of ionic soluble supports allows for selectiveprecipitations of the growing oligonucleotide over all other reagentsused in the oligonucleotide synthesis cycle.

To date, there have been many attempts to design protecting groups andmethods that embody the conditions required for the construction of highquality oligoribonucleotides [for reviews, see Beaucage, S. L. Curr.Opin. Drug Discov. Devel. 11, 203-16 (2008); Reese, C. B. Organic &Biomolecular Chemistry 3, 3851-3868 (2005)]. In fact, for many years,RNA synthesis has been regarded as far more complicated than DNAsynthesis because of the difficulty in finding a compatible2′-protecting group that (a) affords high step-wise coupling yields, (b)is stable throughout chain assembly, and (c) can be removed selectivelyat the end of synthesis without phosphodiester bond isomerization ordegradation.

The most widely used 2′-protecting group is the2′-O-t-butyldimethylsilyl (TBDMS) group [Ogilvie, K. K. et al.Tetrahedron Letters 15, 2861-2867 (1974)]. This protecting group isremoved at the end of RNA chain assembly in the presence of fluorideions. Other silyl ether based protecting groups described for theprotection of nucleosides are triisopropylsilyl (TIPS),methyldiisopropylsilyl (MDIPS), cyclic alkylsilyl and other silyl groups[Ogilvie, K. K. et al. J. of Carbohydrates, Nucleosides, Nucleotides 3,197-227 (1976); Damha M. J, Ogilvie K. K. (1993), Oligoribonucleotidesynthesis: the silyl-phosphoramidite method. In: Protocols forOligonucleotides and Analogs: Synthesis and Properties, Methods inMolecular Biology (Agrawal S, ed.) Vol. 20. Totowa, N.J.: The HumanaPress Inc. pp. 81-114]. Among these, TIPS protection has been describedprimarily for 5′-O-monomethoxytrityl N2-isobutyrylguanosine derivativesas the 2′ and 3′-O-TIPS isomers are more readily separated from eachother by silica gel chromatography [Damha M. J, Ogilvie K. K. (1993),Oligoribonucleotide synthesis: the silyl-phosphoramidite method. In:Protocols for Oligonucleotides and Analogs: Synthesis and Properties,Methods in Molecular Biology (Agrawal S, ed.) Vol. 20. Totowa, N.J.: TheHumana Press Inc. pp. 81-114; Damha, M. J. et al. Tetrahedron Letters45, 6739-6742 (1992)]. The smaller steric bulk of the TBDMS grouprelative to TIPS, TBDPS and other bulkier silyl ethers would favor theTBDMS protecting group, which has been used the most compared to otherprotecting group for RNA synthesis. Coupled with the phosphoramiditecondensation-procedure, 2′-O-TBDMS monomers have allowed a highlyefficient synthesis of oligoribonucleotides [Ogilvie, K. K. et al. Proc.Natl. Acad. Science (USA), 85, 5764-5768 (1988); Usman, N. et al. J. Am.Chem. Soc. 109, 7845-7854 (1987)].

A potential drawback of silyl ethers for the protection of the2′-hydroxyl group lies in their widely recognized ability to undergo2′-to-3′ isomerization under the influence of protic solvents,nucleophilic catalysts, or basic conditions. For example, the TBDMSgroup migrates from the O2′ to O3′ position (and vice versa) in thepresence of either methanol, imidazole, pyridine/water, or aqueousammonia, thereby generating a mixture of nucleoside O2′ and O3′ silylregioisomers [Ogilvie, K. K. and Entwistle, D. W. Carbohydrate Res. 89,203-210 (1981); Ogilvie, K. K. (1983) Proceedings of the 5thInternational Round Table on Nucleosides, Nucleotides and TheirBiological Applications, (Rideout, J. L. et al. eds.), Academic, London,pp. 209-256); Damha M. J, Ogilvie K. K. (1993), Oligoribonucleotidesynthesis: the silyl-phosphoramidite method. In: Protocols forOligonucleotides and Analogs: Synthesis and Properties, Methods inMolecular Biology (Agrawal S, ed.) Vol. 20. Totowa, N.J.: The HumanaPress Inc. pp. 81-114].

Silyl isomerization is characteristic of other O-silyl ether protectinggroups. O-TIPS derivatives of uridine and 7-deazaguanosine also undergoisomerization in methanol, albeit more slowly than their O-TBDMScounterparts [Ogilvie, K. K. et al. J. or Carbohydrates, Nucleosides,Nucleotides 3, 197-227 (1976); Seela, F. and Mersmann, K., HelveticaChimica Acta, 76, 1435-1449(1993)].5′-O-Monomethoxytrityl-N2-isobutyryl-2′-O-TIPS guanosine undergoesisomerization under ethanolic aq. ammonia conditions to give a mixtureof 2′/3′-TIPS regioisomers which can be separated by chromatography.This provides a method to convert (recycle) more of the unwanted3′-isomer into the more useful 2′-isomer [Damha M. J, Ogilvie K. K.(1993), Oligoribonucleotide synthesis: the silyl-phosphoramidite method.In: Protocols for Oligonucleotides and Analogs: Synthesis andProperties, Methods in Molecular Biology (Agrawal S, ed.) Vol. 20.Totowa, N.J.: The Humana Press Inc. pp. 81-114].

2′-O-Silyl groups do not normally migrate to 03′ in dry aprotic solvent.When these conditions are strictly adhered to it is possible to prepare2′-O-silylated ribonucleoside-3′-O-phosphoramidite derivatives inregiosomerically pure form [Milecki, J. et al. Nucleosides &Nucleotides, 8, 463-474 (1989); Scaringe, S. A. et al. Nucleic AcidsRes., 18, 5433-5341 (1990)]. This is clearly an important requirement asthe presence of even traces of the 3′-O-silyl regioisomer will impact onthe quality and biological activity of the desired RNA sequence.

Many other protecting groups for the 2′-hydroxyl position have been usedin the synthesis of RNA [reviewed in Beaucage, S. L. Curr. Opin. DrugDiscov. Devel. 11, 203-16 (2008); Reese, C. B. Organic & BiomolecularChemistry 3, 3851-3868 (2005)]. RNA synthesis using monomers containingthe 2′-triisopropylsilyloxymethyl (TOM) group, the 2′-acetal-levulinylgroup, and the 2′-O-bis(2-acetoxyethoxy)methyl (ACE) group, have beenreported to yield higher coupling efficiency, because these protectinggroups exhibit lower steric hindrance than the 2′-TBDMS group [for acomparative study, see Lackey, J. G. et al. J. Am. Chem. Soc. 131,8496-8502 (2009)]. Like the TBDMS group, the TOM protecting group isremoved using fluoride.

In all cases the synthesis of oligoribonucleotides is an elaboratemultistep process, which entails assembly of the oligonucleotide chaintypically from monomeric phosphoramidite building blocks (e.g.,5′-O-dimethoxytrityl-N-protected-2′-O-tert-butyldimethylsilyl-nucleoside-3′-O-phosphoramidites),deprotection of the base labile nucleobase protecting groups (e.g.,benzoyl, isobutyryl, acetyl, phenoxyacetyl, levulinyl, etc.), cleavagefrom the support (e.g., glass beads or polystyrene), followed by removalof the 2′-hydroxyl protecting group.

The generation of oligoribonucleotide blocks is more difficult due tothe presence of the 2′-hydroxyl group and the protection it requires,thus this line of research has also lagged far behind that of DNAblocks. Nevertheless, there have been several reports describing thesynthesis of RNA through block coupling condensation reactions. Ikeharaand co-workers coupled RNA trimer and tetramers using thephosphotriester method to give 30% yield after several days [Ohtsuka, E.et al. J. Am. Chem. Soc. 100, 8210 (1978)]. Werstiuk and Nielsonreported the coupling of an RNA tetramer and an RNA pentamer affordingthe desired nonanucleotide RNA sequence in 50% yield after 16 days[Werstiuk, E. S., Neilson, T. Can. J. Chem. 54, 2689 (1976)]. Van Boomand co-workers condensed an RNA tetramer and an RNA decamer in 58% yieldin a 3.5 days reaction [van Boom, J. H. et al. Tray. Chim. Pays-Bas, 97,73 (1978)]. Ogilvie and co-workers described the synthesis of5′-O-monomethoxytrityl-2′-O-tert-butyldimethylsilyl-3′-O-levulinylribonucleoside monomers and their use in the assembly of ahexadecauridylic acid via the phosphodichloridite procedure [Nemer, M.J, and Ogilvie, K. K., Can. J. Chem. 58, 1389-1397 (1980)].

Solid-phase RNA synthesis is carried out almost exclusively usingmonomeric phosphoramidite synthons. Given the efficiency of thephosphoramidite chemistry, it is highly desirable to have access toblock (dimer and trimer) phosphoramidites for RNA synthesis, as thesewould permit longer chain extensions at each step during chain assembly,significantly shortening the time required for synthesis.

However, while solid-supported synthesis overcomes the limitation ofpurification by allowing excess reagents to be washed away, it can bequite restricting in terms of scale. While it is true that current largescale methods of producing oligonucleotides in the kilogram scaleutilize solid phase approaches, the mechanical requirements for thistype of manufacturing are very specialized and costly. Therefore, anideal method of large scale synthesis is in solution. In attempts toovercome this limitation, a variety of soluble polymer-based supportshave been developed [Gravert, D. J., Janda, K. D. Chem. Rev. 97, 489-509(1997)]. These however suffer from their own limitations such as poorloading, unfavorable atom economy, and the reliance on temperaturecycling to solvate/precipitate the soluble support. Some uniqueperfluorinated “supports” have been reported that are covalentlyattached to a desired molecule and hence adhere to long chainfluorocarbon derivatized silica. They can be selectively removed byperfluorinated solvents. This is a very efficient process, but requiresmany specialized and expensive materials [Horvath, I. T., Rabai, J.Science, 266, 72-75. (1994); Studer, A. et al., Science, 275, 823-826,(1997)].

It is also desirable therefore to have improved methods for solutionphase RNA synthesis.

SUMMARY OF THE INVENTION

Methods for the synthesis of blockmer (dimer, trimer, tetramer, etc.)ribonucleotides that have applications in the synthesis of RNA throughblock coupling reactions are described herein. These building blocksallow longer chain extensions at each coupling stage of RNA synthesis,significantly reducing the total number of steps required in thesynthesis of a target RNA oligomer. Additionally, the block couplingstrategy disclosed herein produces crude RNA oligomers that are morereadily separated from shorter failure sequences. The procedure isillustrated by the synthesis of UpU, ApA, and UpUpU blocks and their usein the assembly of oligoribonucleotide chains via a phosphoramiditecoupling method. The disclosed compounds and processes benefit twocritical aspects of siRNA manufacturing: speed, and purity of a targetoligomer.

In another aspect, methods for the synthesis of blockmer (dimer, trimer,tetramer, etc.) deoxyribonucleotides that have applications in thesynthesis of DNA through block coupling reactions are described herein.These building blocks allow longer chain extensions at each couplingstage of DNA synthesis, significantly reducing the total number of stepsrequired in the synthesis of a target DNA oligomer. Additionally, theblock coupling strategy disclosed herein produces crude DNA oligomersthat are more readily separated from shorter failure sequences.

There are provided herein methods for the synthesis of ionically taggedlinkers for, but not limited to, the synthesis of oligoribonucleotides,oligodeoxyribonucleotides, oligopeptides and oligosaccharides, which canbe orthogonally cleaved in the presence of all other standard protectinggroups. Tag-linker combinations provided herein make it possible to growoligonucleotides in solution using stepwise iterative couplings,utilizing the ionic properties of the tags to selectively precipitate agrowing oligonucleotide at each step, in order to remove couplingreagents and reactants. Tag-linkers enable removal of a synthesizedoligonucleotide from solution at any point in the synthesis, to producea free 3′-O-hydroxyl, 2′-TIPS protected oligomer, without anyisomerisation of the 2′-O-silyl protecting group. This can be utilizedfor, but not limited to, converting an oligomer (dimer, trimer,tetramer, etc.) into block-phosphoramidites. These building blocksenable longer chain extensions at each coupling stage of RNA or DNAsynthesis, significantly reducing the total number of steps required inthe synthesis of a target RNA or DNA oligomer. Additionally, the blockcoupling strategy produces crude RNA or DNA oligomers that are readilyseparable from shorter, undesired sequences that arise during synthesis.It is also envisioned that, in some embodiments, tag linkers can be usedin place of standard ester protecting groups, to provide both a mildcleavage alternative as well as a means to selectively precipitate adesired molecule and circumvent the use of costly and time consumingchromatography.

In one aspect, there is provided a compound of formula (II):

whereinn is an integer from 1 to 19;R₁ is a protecting group;R₃ is selected from H, a protecting group, or

R₅ is selected from H, or a protecting group;R_(p) is a protecting group;R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine, or asubstituted cyclic alkylamine, preferably morpholine;B is a nitrogen-containing base;wherein each B, R₁ and R_(p) may be the same or different from any otherB, R₁ and R_(p), respectively.

In another aspect, there is provided a process for preparing a compoundof formula (II):

whereinn is selected from 1, 2, or 3;R₁ is a protecting group;R₃ is selected from H or a protecting group;R₅ is a protecting group;R_(p) is a protecting group;B is a nitrogen-containing base;wherein each B, R₁ and R_(p) may be the same or different from any otherB, R₁ and R_(p), respectively;the process comprising the steps of:a) condensing a phosphoramidite of formula (III):

-   -   wherein B, R₁, R₅, and R_(p) are as defined above; and    -   R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine, or        a substituted cyclic alkylamine, preferably morpholine;        with a nucleoside of formula (IV):

wherein B and R₃ are as defined above; andb) oxidizing the product of step (a) to produce the compound of formula(II) where n is 1, and B, R₁, R₃, R₅, and R_(p) are as defined above;andc) where n>1, the process further comprising:

-   -   (i) deprotecting the terminal —OR₅ group of the product of the        previous step to form a free 5′-OH group;    -   (ii) condensing the product of step (i) with a phosphoramidite        of formula (III), wherein B, R₁, R₅, R_(p) and R are as defined        above, and each B, R₁, R₅, R_(p) and R may be the same or        different from any other B, R₁, R₅, R_(p) and R, respectively;    -   (iii) oxidizing the product of step (ii);    -   (iv) repeating steps (i)-(iii) n−2 times;        to form the compound of formula (II).

In an aspect, there is provided herein an ionic tag linker comprising agamma ketoester moiety, an ionic moiety and a linker. In one embodiment,the ionic tag linker has the structure of formula (K):

The linker may be, for example, alkyl, glycol or functionalized alkyl.In some embodiments, alkyl is C1 to C6 alkyl. The ionic moiety may be,for example, an imidazolium or phosphonium group. In some embodiments,an ionic moiety comprises a halide, for example an ionic moiety maycomprise Br⁻, Cl⁻ or I⁻.

It should be understood that an ionic moiety in an ionic tag linker ofthe invention may comprise any salt, such as but not limited to aphosphonium salt, an imidazolium salt, etc. Many salts are known in theart and are within the capacity of a skilled technician. Furthernon-limiting examples include organic salts comprising a heterocyclic orsubstituted heterocyclic quaternary nitrogen-containing organic cation,a heterocyclic or substituted heterocyclic quaternary phosphoniumcontaining organic cation, or a heterocyclic or substituted heterocyclictrivalent sulfonium containing organic cation; and an anion balancingthe charge on the organic cation. In a more particular embodiment anorganic cation is selected from the group consisting of N-substitutedpyridine and 1,3-disubstituted imidazole. An anion balancing the chargeon the organic cation may be selected from the group consisting of Cl″,Br′, BF4″, PF6″, SbF6″, CuCl2″, I and AICI4″. Other suitable anionscould also be used and are well within the capacity of a skilledtechnician.

In an embodiment, an ionic moiety in an ionic tag linker of theinvention is a zwitterionic phosphonium salt of Formula I:

wherein: n is 0 or 1; R is H or SO₃ ⁻; R′ is selected from the groupconsisting of C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₁₀ alkynyl, C₃-C₁₀cycloalkyl, phenyl, substituted phenyl, benzyl and C₁-C₁₀alkoxycarbonyl; R′ is CX₃ when n is 0; and X is selected from the groupconsisting of F, Cl, Br and I. For example, the zwitterionic phosphoniumsalt may have the following structure:

In an embodiment, a gamma ketoester moiety is cleavable with hydrazine.

In another aspect, there is provided herein an ionic tag linkercomprising a photolabile moiety, an ionic moiety and a linker. Thephotolabile moiety may be, for example, a nitrobenzyl derivative. In anembodiment, the ionic tag linker has the structure of formula (P):

wherein X is N or O.

The linker may be alkyl, glycol or functionalized alkyl. In someembodiments, alkyl is C₁ to C₆ alkyl. The ionic moiety may be animidazolium or phosphonium group. In one embodiment, the photolabilemoiety is cleavable by photolysis.

In some embodiments, ionic tag linkers provided herein are orthogonallycleavable. In further embodiments, ionic tag linkers are attached to theterminal 3′-hydroxyl of an oligoribonucleotide oroligodeoxyribonucleotide. Ionic tag linkers may be selectively cleavableunder conditions which do not cleave other oligoribonucleotide oroligodeoxyribonucleotide protecting groups. Ionic tag linkers may alsobe cleavable under conditions which do not cause isomerisation of, e.g.,terminal oligoribonucleotide 2′-O-silyl protecting groups.

In an embodiment, an ionic tag linker is selected from:

wherein X is selected from NH and O.

In another embodiment, an ionic tag linker is selected from:

compound (17); compound (25); compound (32); compound (43);compound (55); compound (57); compound (23); compound (56);compound (54); compound (76); compound (7); compound (8);compound (9); compound (15); compound (16); compound (19);compound (70); compound (80); compound (82); and compound (10).

In an embodiment, an ionic tag linker comprises a diethoxy group or adithiophenyl group. In a particular embodiment, an ionic tag linkercomprises a dithiophenyl group and a phosphonium salt. In anotherembodiment, an ionic tag linker comprises a dithiophenyl group and animidazolium salt. In yet another embodiment, an ionic tag linkercomprises a diethoxy group and a phosphonium salt. In a furtherembodiment, an ionic tag linker comprises a diethoxy group and animidazolium salt.

In another aspect, there are provided herein compounds of formula (II):

wherein:n is an integer from 1 to 19;R₁ is a protecting group;R₃ is selected from H, a protecting group,

and an ionic tag linker provided herein;R₅ is selected from H, and a protecting group;R_(p) is a protecting group;R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine or asubstituted cyclic alkylamine, preferably morpholine; andB is a nitrogen-containing base;wherein each B, R₁ and R_(p) may be the same or different from any otherB, R₁ and R_(p), respectively.

In an embodiment, n is 1, 2, or 3. In another embodiment, R₃ is

and R₅ is a protecting group. In yet another embodiment, R₃ is

R₅ is selected from DMTr or MMTr; R_(p) is selected from methyl (Me),2-cyanoethyl (CNEt), ortho-chlorophenyl (o-ClPh), and para-chlorophenyl(p-ClPh); R is selected from isopropyl, methyl, and ethyl; and B is anucleobase protected on at least one nitrogen by a suitable N-protectinggroup. In a still further embodiment, R is isopropyl. In anotherembodiment, a N-protecting group is selected from levulinyl, acetyl,difluoroacetyl, trifluoroacetyl, isobutyryl, benzoyl,9-fluorenylmethoxycarbonyl, phenoxyacetyl, dimethylformamidine, andN,N-diphenyl carbamate.

In some embodiments, R₃ is substituted with an ionic tag linker providedherein. In embodiments, R₃ is

or a protecting group, and may or may not be substituted with an ionictag linker provided herein. In another embodiment, the protecting groupis a levulinyl group (Lev), or is an ionic tag linker provided herein,e.g., an ionic tag linker comprising a gamma ketoester moiety or anionic tag linker comprising a photolabile moiety.

In another aspect, there are provided herein processes for preparingcompounds disclosed herein. In an embodiment, a compound has thestructure:

wherein:n is selected from 1, 2, and 3;R₁ is a protecting group;R₃ is selected from H, a protecting group and an ionic tag linkerprovided herein;R₅ is a protecting group;R_(p) is a protecting group; andB is a nitrogen-containing base;wherein each B, R₁ and R_(p) may be the same or different from any otherB, R₁ and R_(p), respectively;and a process comprises the steps of:a) condensing a phosphoramidite of formula (III):

-   -   wherein B, R₁, R₅, and R_(p) are as defined above; and    -   R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine, or        a substituted cyclic alkylamine, preferably morpholine;    -   with a nucleoside of formula (IV):

-   -   wherein B and R₃ are as defined above; and        b) oxidizing the product of step (a) to produce the compound of        formula (II) where n is 1, and B, R₁, R₃, R₅, and R_(p) are as        defined above; and        c) where n>1, the process further comprising:    -   (i) deprotecting the terminal —OR₅ group of the product of the        previous step to form a free 5′-OH group;    -   (ii) condensing the product of step (i) with a phosphoramidite        of formula (III), wherein B, R₁, R₅, R_(p) and R are as defined        above, and each B, R₁, R₅, R_(p) and R may be the same or        different from any other B, R₁, R₅, R_(p) and R, respectively;    -   (iii) oxidizing the product of step (ii); and    -   (iv) repeating steps (i)-(iii) n−2 times;        to form the compound of formula (II).

In an embodiment, R₃ is H. In another embodiment, R₃ is a protectinggroup, and the process further comprises: d) removal of the R₃protecting group. In an embodiment, the protecting group is a levulinyl(Lev) group. In another embodiment, the protecting group is an ionic taglinker provided herein.

In other embodiments, processes of the invention further comprisephosphitylation of the product of step (b) or (c) to form a compound offormula (IIa):

wherein n, B, R₁, R₅, R_(p) and R are as previously defined.

Processes may also comprise phosphitylation of the product of step (d)to form a compound of formula (IIa):

wherein n, B, R₁, R₅, R_(p) and R are as previously defined.

In an embodiment, R₁ is TBDMS; R₅ is selected from DMTr and MMTr; R_(p)is selected from methyl (Me), 2-cyanoethyl (CNEt), ortho-chlorophenyl(o-ClPh), and para-chlorophenyl (p-ClPh); R is selected from isopropyl,methyl, and ethyl; and B is a nucleobase protected on at least onenitrogen by a suitable N-protecting group, wherein the N-protectinggroup is selected from levulinyl, acetyl, difluoroacetyl,trifluoroacetyl, isobutyryl, benzoyl, 9-fluorenylmethoxycarbonyl,phenoxyacetyl, dimethylformamidine, and N,N-diphenyl carbamate.

In further aspects, there are provided herein methods for synthesizingan oligomer, the methods comprising: (a) attaching an ionic tag linkerprovided herein to a first monomer unit; (b) contacting the firstmonomer unit with at least one further monomer unit at reactionconditions to provide an oligomer comprising from 2 to 30 monomer units;and (c) cleaving the ionic tag linker from the oligomer to provide thefree oligomer. In an embodiment, the oligomer is an oligopeptide, anoligosaccharide or an oligonucleotide. In a particular embodiment, theoligonucleotide is an oligoribonucleotide. In another embodiment, theoligonucleotide is an oligodeoxyribonucleotide.

In one embodiment, there is provided a method for synthesizing anoligoribonucleotide, the method comprising: (a) attaching an ionic taglinker provided herein to a first ribonucleoside at the terminal3′-hydroxyl; (b) contacting the first ribonucleoside with at least onefurther ribonucleoside at reaction conditions to provide anoligoribonucleotide comprising from 2 to 30 ribonucleosides; and (c)cleaving the ionic tag linker from the oligoribonucleotide to providethe free oligoribonucleotide.

In some embodiments, methods provided herein further comprise a step ofisolating an oligomer, oligoribonucleotide or oligodeoxyribonucleotidebefore cleaving an ionic tag linker from the oligomer,oligoribonucleotide or oligodeoxyribonucleotide. For example, anoligomer, oligoribonucleotide or oligodeoxyribonucleotide may beisolated by precipitation, based on ionic properties of an ionic taglinker.

In another aspect, there is provided herein a ribonucleoside havingattached at its 3′-hydroxy an ionic tag linker provided herein.

In yet another aspect, there is provided herein a deoxyribonucleosidehaving attached at its 3′-hydroxy an ionic tag linker provided herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a ³¹P-NMR spectrum of compound (30) (4 P-diastereomers) inCD₃CN.

DETAILED DESCRIPTION OF THE INVENTION

The present disclosure relates generally to the field of oligonucleotidesynthesis, and provides compositions and methods for the synthesis ofRNA and DNA. In some embodiments, novel dimer and trimer blocks areprovided for the synthesis of RNA or DNA oligonucleotides on solidsupports. In another embodiment, a tetramer block is provided. In yetanother embodiment, larger blockmers are provided (e.g., 5-, 6-, 7-, 8-,9-, 10-, 11-, 12-, 13-, 14-, 15-, 16-, 17-, 18-, 19-, or 20-mers). Infurther aspects, ionic tags for liquid phase synthesis and methods forliquid or solution phase synthesis of oligomers, e.g., oligopeptides,oligosaccharides, oligonucleotides, particularly RNA oligonucleotidesand also DNA oligonucleotides, are provided.

In a standard oligonucleotide synthesis cycle, chain elongation beginswith the selective cleavage of the 5′-O-dimethoxytrityl (DMTr) group byan organic acid (e.g., TFA), liberating a free 5′-hydroxyl group. Thisterminal nucleophile is then allowed to couple to a protected nucleoside3′-O-phosphoramidite monomer in the presence of an activator. In thecase of RNA synthesis, suitable protection of the 2′-hydroxyl group isrequired to prevent side reactions. Any unreacted 5′-hydroxyl groups areacetylated in a process referred to as ‘capping’, in order to preventelongation of short-mers. The most common capping strategy utilizesacetic anhydride to produce an acetyl ester “cap”. Thus, ‘capping’esterifies any unreacted 5′-hydroxyl groups, and prevents theaccumulation of by-products. The newly created phosphite triester3′,5′-linkage is then oxidized to produce the more stable phosphatetriester. This process is repeated until an oligomer of a desired lengthand sequence is obtained. Cleavage of the oligomer from a solid support,and removal of all protecting groups from the sugars, phosphates andnucleobases, provides the desired target oligomer, which is thenpurified from shorter undesired sequences by ion exchange highperformance liquid chromatography (HPLC), ion-pair reverse phase HPLC,or polyacrylamide gel electrophoresis (PAGE). A full length oligomer isthen characterized by mass spectrometry. For high throughput synthesisapplications, a very large number of DNA or RNA oligomers can besynthesized in parallel on DNA and RNA microarrays or “gene chips”[Ramsay G., Nature Biotechnology 16, 40-44 (1998)], although thesemethods are currently limited to the picomolar scale [Sriram Kosuri etal. Nature Biotechnology, 28, 1295-1299 (2010)].

Unlike a TBDMS group, ACE and TOM protecting groups are not shown tomigrate to vicinal hydroxyl groups in the presence of mild base oraqueous polar protic solvents. While both overcome the isomerisationproblem possessed by TBDMS groups, only ACE protecting groups areorthogonal (with respect to cleavage) to all other protecting groupsused in standard ribonucleoside protection. This is a property that ishighly desirable in RNA synthesis. A TOM protecting group, like mostsilyl protecting groups, is fluoride labile, whereas hydrazine hydratebuffered in pyridine acetic acid will selectively remove the gamma-ketoester of the acetal levulinyl ester (ALE) protecting group, withoutcleaving the dimethoxytrityl, N-benzoyl, methoxy-phosphate or silylprotecting groups used in standard oligoribonucleotide synthesis.

More recently, we have shown 2′-O-TIPS protecting groups can be used asan alternative to 2′-O-TBDMS. This allowed for cleavage of the3′-hydroxyl protecting group, levulinyl, or ALE using buffered hydrazinehydrate, without isomerisation of the 2′-TIPS. This was previouslydetermined to be prohibitive with the TBDMS group when cleaving3′-hydroxyl protecting groups on ribonucleotide dimer and trimer blocks,as isomerisation was found to occur and separation of one regio-isomerover the other was not possible. The same effect could be achieved withTOM protecting groups, but the cost and availability of TIPS-chloridemakes it a superior choice. This led to the production of isomericallypure “block” ribonucleotide phosphoramidites and their utility duringsolid supported oligo synthesis, resulting in higher overall yields,fewer coupling steps, and simplified purification protocols, asdescribed herein.

Solid-supported synthesis overcomes the limitation of purification byallowing excess reagents to be washed away. Unfortunately, it can bequite restricting in terms of scale. While it is true that current largescale methods of producing oligonucleotides in the kilogram scaleutilize solid phase approaches, the mechanical requirements for thistype of manufacturing are very specialized and costly. Therefore, anideal method of large scale synthesis is in solution. An improvementover the polymer based soluble supports was accomplished with use ofionic soluble supports, first described by Tak-Hang Chan for synthesisof carbohydrates and peptides [Chan, T-H. et al. J. Org. Chem., 70,3251-3255 (2005); Chan, T-H. et al. Acc. Chem. Res. 39: 897-908 (2006)].Soluble ionic tags, in contrast to polymer based alternatives, can beprecipitated at room temperature in standard, commercially availablesolvents. These involve simple, inert, readily available ionic species,and they do not suffer from low loading and poor atom economy as seenwith traditional soluble supports. This method of product isolation istherefore beneficial with respect to both cost and time when purifyingcompounds, as it can circumvent the use of chromatography traditionallyused to purify organic compounds. Ionically-tagged molecules could openup synthetic routes once thought to be prohibitively expensive due topurification costs.

Using an ionic tag in place of traditional solid support, a similariterative method of DNA and RNA oligonucleotides synthesis on solidsupport, has been applied recently in solution [Donga, R. A. et al., J.Org. Chem. 71, 7907-7910 (2006); Donga, R. A. et al., Can. J. Chem. 85,274-282 (2007)]. Use of ionic soluble supports allows for selectiveprecipitation of growing oligonucleotide over all other reagents used inthe oligonucleotide synthesis cycle, significantly simplifyingintermediate purification steps. This selective precipitation ofproducts over reagents can be used in a variety of reactions, and hasbeen shown to be effective as an alternative to chromatography. This canbe advantageous, particularly in the context of a large scale industrialprocess where chromatography can be prohibitively expensive [Chan, T-H.et al. J. Org. Chem., 70, 3251-3255 (2005); Chan, T-H. et al. Acc. Chem.Res. 39: 897-908 (2006)].

Thus, we sought to combine a process of solution phase oligonucleotidesynthesis using a soluble ionic-tag approach to produce blocknucleotide, e.g., ribonucleotide, phosphoramidites, in particular toovercome at least some or all of the limitations of solid phasesynthesis, which can be long and tedious.

Traditionally, the free 3′-hydroxyl group has been protected/linked to asolid support by an ester bond through a succinyl linker to a long chainalkyl amine derivatised to a solid support. This would remain covalentlybound during the iterative stepwise synthesis of DNA, RNA, peptides oroligosaccharides. This covalent bond is cleaved at the end of thesynthesis by amminolysis, which simultaneously cleaves other protectinggroups (cyanoethyl and exocyclic amine base protecting groups for DNAand RNA) throughout the molecule. A fully deprotected molecule isreleased in the case of DNA and peptide synthesis, or a partiallydeprotected molecule in the case of RNA and some oligosaccharides[Beaucage, S. L.; Herdewijn, P. Curr. Protoc. Nucleic Acid Chem.47:13.0-13.4 (2011)]. This multi-cleavage event is of great utility whenthe full deprotection of the final molecule is desired, but can betroublesome when the desired molecule must retain its protecting groupsfor further modifications or transformations post-oligomerization.

A variety of different linkers have now been developed for attachingnucleosides to their solid supports. A particularly versatile linker,Uny-linker™, is widely used because it does not require derivatizationof a nucleoside to the support prior to automated oligonucleotidesynthesis. Other alternatives include the Q-linker developed by Pon andco-workers [Pon, R. T., Yu, S. Nucleic Acids Research 25, 3629-3635(1997)] and silicon-based linkers, which are cleaved by a fluoridesource via pyridine-HF [Boehm T. L., Showalter, H. D. H., J. Org. Chem.,61 6498-6499 (1996)]. Additionally, a variety of photolabile linkersbased on the nitrophenyl group have been reported and used for manysensitive applications [Anderson, E., et al. Nucleosides, Nucleotidesand Nucleic Acids, 22, 1403-1406 (2003); Pirrung, M. C. et al. Org Lett,3, 1105-1108 (2001); Pfeiderer, W. et al. Nucleosides and Nucleotides,17, 1987-1996 (1998)].

A levulinyl group in the place of traditional esters at the 3′-hydroxylcan be removed in conjunction with a 2′-TIPS protecting group withoutisomerisation allowing for chemical modifications following-chainelongation [Hassler, M. H. et al. Tett Lett, 52, 2575-2578 (2011);Nemer, M. J, and Ogilvie, K. K., Can. J. Chem. 58, 1389-1397 (1980)].The levulinyl group possesses the same stability as traditional esters,but can be cleaved by mild treatment with buffered hydrazine. Thismethod is compatible with all protecting groups used in DNA and RNAsynthesis, as well as many protecting groups used in classical syntheticorganic chemistry. Exceptions are any molecules bearing an unprotectedketone functional group, as hydrazine will readily react to form ahydrazone. This is fundamental in the cleavage mechanism of thelevulinyl protecting group. Unfortunately, a problem with replacing the3′-O-succinyl linker with a levulinyl group is that it is no longerattachable to a solid support. To overcome this issue a levulinyl-likelinker would have to be chemically modified to install functional groupsthat allow for coupling to the ionic tag.

Among all previously developed linkers, a photolabile linker seems tooffer the mildest of conditions. However no photolabile linker waspreviously developed and used to release an oligoribonucleotide from the3′-terminal position, and shown to retain regio-isomeric purity. Such alinker is highly desirable and is provided herein. A NPPOC typephotolabile linker that could be coupled to solid support providedpartially esterified oligoribonucleotides Johnsson, R. et al.,Bioorganic & Medicinal Chemistry Letters, 21, 3721-3725, (2011)].

The options of using linkers which are cleaved under mild conditionswould be of particular interest to those attempting post synthesismodifications of oligonucleotides. To our knowledge, no photolabile orlevulinyl-like linkers have been previously developed and used for DNAand RNA synthesis, which are cleavable in the presence of traditionaloligoribonucleotide protecting groups, which also do not causeisomerisation of the terminal 2′-O-silyl protecting group when thelinker is cleaved from the terminal 3′-hydroxyl.

There are provided herein methods which combine a process of solutionphase oligonucleotide synthesis using a soluble ionic-tag approach toproduce block ribonucleotide phosphoramidites. Methods provided hereinare also applicable to oligodeoxyribonucleotide (oligo DNA) synthesis.For example, there are provided herein methods which combine a processof solution phase oligonucleotide synthesis using a soluble ionic-tagapproach to produce block deoxyribonucleotide phosphoramidites.

Accordingly, we report herein novel linkers that can attach to anionic-tag and the 3′-hydroxyl of a nucleoside with the ability to cleavewithout simultaneous deprotection of any other protecting groups, norcause isomerization of the 2′-silyl group to the 3′-position. In anembodiment, ionic tag linkers are provided herein.

In one embodiment there is provided a compound of formula (II):

whereinn is an integer from 1 to 19;R₁ is a protecting group;R₃ is selected from H, a protecting group, and

R₅ is selected from H, and a protecting group;R_(p) is a protecting group;R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine, or asubstituted cyclic alkylamine, preferably morpholine;B is a nitrogen-containing base;wherein each B, R₁ and R_(p) may be the same or different from any otherB, R₁ and R_(p), respectively.

In another embodiment, n is selected from 1, 2, and 3.

In another embodiment, R₃ is

and R₅ is a protecting group.

In another embodiment:

R₃ is

R_(p) is selected from methyl (Me), 2-cyanoethyl (CNEt),ortho-chlorophenyl (o-ClPh), and para-chlorophenyl (p-ClPh), preferablymethyl, and R is selected from isopropyl, methyl, and ethyl, preferablyisopropyl.

In another embodiment:

R₁ is TBDMS;

R₅ is selected from DMTr and MMTr, preferably DMTr; and

B is a nucleobase protected on at least one nitrogen by a suitableN-protecting group.

In another embodiment, a suitable N-protecting group is selected fromlevulinyl, acetyl, difluoroacetyl, trifluoroacetyl, isobutyryl, benzoyl,9-fluorenylmethoxycarbonyl, phenoxyacetyl, dimethylformamidine, andN,N-diphenyl carbamate.

In another embodiment, R₃ is a protecting group. In yet anotherembodiment, a protecting group is a levulinyl group (Lev). In still yetanother embodiment, a protecting group is an ionic tag linker. Inanother embodiment, an ionic tag linker is selected from:

wherein X is selected from NH and O.

The term “lower alkyl” as used herein refers to acyclic, straight orbranched chain alkyl groups containing from one to six carbons.Preferred lower alkyl groups include, for example, isopropyl, methyl,and ethyl.

Functional groups of compounds disclosed herein may be protected by avariety of protecting groups known to those of skill in the art. A“protecting group” is used in the conventional chemical sense toreference a group which reversibly renders unreactive a functional groupunder specified conditions of a desired reaction. Some protecting groupsare well known to one skilled in the art. Examples of theprotection/deprotection process as well as various protecting groups aredescribed in Wuts and Greene, 2006, Greene's Protective Groups inOrganic Synthesis, Wiley-Interscience, New York, N.Y. Any suitableprotecting group known to one skilled in the art may be used. After thedesired reaction, protecting groups may be removed to deprotect theprotected functional group. All protecting groups should be removable(and hence, labile) under conditions which do not degrade a substantialproportion of the molecules being synthesized. In contrast to aprotecting group, a “capping group” permanently binds to a segment of amolecule to prevent any further chemical transformation of that segment.It should be noted that the functionality protected by the protectinggroup may or may not be a part of what is referred to as the protectinggroup.

For instance, possible protecting groups for R₁ for the compounds offormula (II) above and the various compounds below include:

-   -   1. Fluoride labile protecting groups including:        t-butyldimethylsilyl (TBDMS), triisopropylsilyl (TIPS);        triisopropyloxymethyl (TOM); cyanoethylmethyl (CEM);        2-(4-tolylsulfonyl)ethoxymethyl (TEM).    -   2. Acid labile groups including acetal groups:        2′-O-bis(2-acetoxyethoxy)methyl (ACE) orthoester;        1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp);        1-(4-chlorophenyl)-4-ethoxypiperidin-4-yl (Cpep);        4-(N-dichloroacetyl-N-methylamino) benzyloxymethyl (4-MABOM);        trityl ether groups including dimethoxytrityl (DMTr) and        monomethoxytrityl (MMTr).    -   3. Reduction labile groups including: 2-tert-butyldithiomethyl        (DTM); allyl.    -   4. Base labile groups including: levulinyl (Lev) and acetal        levulinyl (ALE).    -   5. Photolabile groups including: photolabile groups including        nitrobenzyl groups (including 2′-nitrobenzyl groups such as        2-(2-nitrophenyl)propoxycarbonyl (NPPOC),        α-methylnitorpiperonyloxycarbonyl (MeNPOC) and derivatives        therein (including thioxanthone-nitrobenzyl group conjugates)        and 5′-O-dimethoxybenzoincarbonate group (DMBOC).

Possible protecting groups for R₅ for the compounds of formula (II)above and in the various compounds below include 9-phenylxanthyl (pixylor Px) and its derivatives, MMTr, and DMTr. Preferably, these protectinggroups are used for R₅ when options 1, 3, 4, and 5 are used asprotecting groups for R₁ as noted above.

The R_(p) group as shown for the compounds of formula (II) above and inthe various compounds below may be methyl (Me), 2-cyanoethyl (CNEt),p-nitro-phenylethyl (NPE), and para- and ortho-chloro-phenyl (p- oro-ClPh).

Possible protecting groups for the 3′-hydroxyl position (R₃ for thecompounds of formula (II) and for the various compounds described below)include levulinyl, and ionic protecting groups, also referred to asionic tag linkers. Suitable ionic tags are known to those of skill inthe art. These may include those described in PCT ApplicationPublication No. WO 2006/096963 of Chan, T.-H. et al., the contents ofwhich are incorporated herein by reference in its entirety. Suitableionic tags may include, for example, imidazolium and phosphonium ionicmoieties having linkers selected from alkyl linkers, glycol linkers,etc.

In an embodiment, an ionic tag is a phosphonium ionic tag comprising azwitterionic phosphonium salt of Formula I:

wherein: n is 0 or 1; R is H or SO₃ ⁻; R′ is selected from the groupconsisting of C₁-C₁₀ alkyl, C₂-C₁₀ alkenyl, C₂-C₁₀ alkynyl, C₃-C₁₀cycloalkyl, phenyl, substituted phenyl, benzyl and C₁-C₁₀alkoxycarbonyl; R′ is CX₃ when n is 0; and X is selected from the groupconsisting of F, Cl, Br and I. In another embodiment, the zwitterionicphosphonium salt of Formula I is:

These and other zwitterionic phosphonium salts which may be included inionic tags of the invention are described in, for example, InternationalPCT Application Publication No. WO2010/012096, the entire contents ofwhich are hereby incorporated by reference.

In one embodiment, a protecting group is an orthogonally cleavable ionictag linker. For example, a protecting group can be in one embodiment anorthogonally cleavable ionic tag linker (K) comprising a gamma ketoestermoiety, an ionic moiety and a linker:

In another embodiment, a protecting group is an orthogonally cleavableionic tag linker (P) comprising a photolabile moiety, e.g., anitrobenzyl derivative, and an ionic moiety and a linker:

Both (K) and (P) contain an ionic moiety for use in aprecipitation-based purification as described in described in PCTApplication Publication No. WO 2006/096963 of Chan, T.-H. et al., thecontents of which are incorporated herein by reference in its entirety.The ionic moiety in (K) and (P) is attached to a gamma-keto ester orphotolabile moiety, respectively, through a linker, most simply a shortalkyl chain or a functionalized alkyl chain of one or more carbons. Agamma-keto moiety is cleaved selectively with hydrazine, whereas (P), anitrobenzyl derivative, is cleaved by photolysis, releasing the 3′OHgroup for further functionalization. The present invention provides amethod for cleavage of (K) and (P), as well as phosphitylation of theunblocked 3′OH to afford amidite blocks for use in oligonucleotidesynthesis.

The entity B in the compounds of formula (II) above and in the compoundsdescribed below is a nitrogen-containing base, preferably a base or aprotected-base (also referred to herein as a “nucleobase”). The base ispreferably a purine or pyrimidine base or analog thereof. Analogsinclude diaminopurine and its derivatives, inosine and its derivatives,alkylated purines or pyrimidines, acylated purines or pyrimidines, andthiolated purines or pyrimidines. More specific analogs include, forexample, 1-methyladenine, 2-methyladenine, N6-methyladenine,N6-isopentyladenine, 2-methylthio-N6-isopentyladenine,N,N-dimethyladenine, 8-bromoadenine, 2-thiocytosine, 3-methylcytosine,5-methylcytosine, 5-ethylcytosine, 4-acetylcytosine, 1-methylguanine,2-methylguanine, 7-methylguanine, 2,2-dimethylguanine, 8-bromoguanine,8-chloroguanine, 8-aminoguanine, and the like. A “protected base” isprotected on at least one nitrogen by any suitable N-protecting groupincluding levulinyl, acetyl, difluoroacetyl, trifluoroacetyl,isobutyryl, benzoyl, 9-fluorenylmethoxycarbonyl, phenoxyacetyl,dimethylformamidine, N,N-diphenyl carbamate, and the like. Preferably,the base is selected such that the compound of formula (II) is aderivative of adenine (A), cytosine (C), guanine (G), or uracil (U). Inan embodiment, where the compound is a deoxyribonucleotide, the base isselected such that the compound of formula (II) is a derivatice ofadenine (A), cytosine (C), guanine (G), or thymine (T).

Various aspects related to the practice of the present invention aredisclosed in PCT International Application Publication No. WO2009/064115 to Samchully Pharm. Co., Ltd.; Kumar, G. and Poonian, M. S.J. Org. Chem., 49, 4905-4912 (1984); Nemer, M. J, and Ogilvie, K. K.,Can. J. Chem. 58, 1389-1397 (1980). Recent advances in RNA synthesishave been summarized in a review by S. Beaucage, Curr. Opin. DrugDiscov. Devel. 11, 203-261 (2008)].

The use of previously reported dimer and trimer phosphoramidite synthonswere directed at the synthesis of RNA oligomers, involving the use ofsuch dimer or trimer units only in the first coupling reaction on solidsupports (WO 2009/064115). Following coupling of one such dimer unit,the ensuing steps involved the exclusive coupling of monomericphosphoramidite units until the desired length was produced (WO2009/064115). This discourages the use of “various kinds of dimers” forthe purpose of RNA synthesis, as this would require “long-term periodsof synthesis and high production costs.” The disclosure furtheremphasizes that it “employs just one dimer or trimer species only in thefirst coupling step and then common inexpensive monomer units in thesubsequent steps, which enable the low-cost, high purity production ofthe nucleotide oligomers”.

In contrast to the above disclosure, the RNA dimers and trimerspresently described can be used exclusively or in combination withmonomeric units. In addition to applications in solution-phase RNAsynthesis, their use can also be extended to routine synthesis of RNA onconventional solid supports such as controlled pore glass andpolystyrene. In this case, the RNA strand is assembled by several blockcouplings, cleaved and released from the support after synthesis and theresulting synthetic RNA utilized in physicochemical or biologicalstudies. There are several derivatives that may be included for suchblock coupling reactions [see structures (30), (47) and (50) below]. The2′-TIPS protecting group at the 3′-termini of such structures providesunique 5′-DMTr 3′-phosphoramidite dimer and trimer synthons for RNAsynthesis. In some embodiments, the methods provided herein are adaptedfor use in solution-phase DNA synthesis as well as routine synthesis ofDNA on conventional solid supports.

Furthermore, the 2′-TIPS protected dimer and trimer synthons describedherein provide several distinct advantages over previously reported2′-TBDMS 3′-phosphoramidite dimer synthons (WO 2009/064115). Theinventors have discovered that the use of TIPS completely eliminates 2′to 3′-isomerization that occurs with 2′-TBDMS protecting groups presentin previously reported synthons (WO 2009/064115); in fact, the presentdisclosure teaches that when synthetic procedures are followed asdescribed in WO 2009/064115, that 2′-TBDMS dimer synthons are notisolated in pure form, but rather as mixtures of 2′+3′-TBDMSregioisomers that are difficult (if not impossible) to separate underthe specifications provided.

In an embodiment, methods described herein provide isomerically puredimer and trimer synthons in high yields. In another embodiment, methodsprovided herein lead to high fidelity RNA synthesis. Such dimer andtrimer synthons when coupled in solution or solid phase, allow longerchain extensions at each coupling stage of RNA synthesis, significantlyreducing the total number of steps required in the synthesis of targetRNA oligomers, and reducing their exposure to acidic environment.Additionally, dimer and trimer synthetic routes produce crude RNAoligomers that are generally more readily separated from the products offailure couplings. Thus the dimer and trimer block approachespotentially benefit critical aspects of siRNA manufacturing: speed andpurification of synthesis, and the integrity of the desired full lengthRNA chain.

In another embodiment, there is provided a process for preparing acompound of formula (II):

whereinn is selected from 1, 2, or 3;R₁ is a protecting group;R₃ is selected from H, a protecting group and an ionic tag linker;R₅ is a protecting group;R_(p) is a protecting group;B is a nitrogen-containing base;wherein each B, R₁ and R_(p) may be the same or different from any otherB, R₁ and R_(p), respectively;the process comprising the steps of:a) condensing a phosphoramidite of formula (III):

-   -   wherein B, R₁, R₅, and R_(p) are as defined above; and    -   R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine, or        a substituted cyclic alkylamine, preferably morpholine;    -   with a nucleoside of formula (IV):

-   -   wherein B and R₃ are as defined above; and        b) oxidizing the product of step (a) to produce the compound of        formula (II) where n is 1, and B, R₁, R₃, R₅, and R_(p) are as        defined above; and        c) where n>1, the process further comprising:    -   (i) deprotecting the terminal —OR₅ group of the product of the        previous step to form a free 5′-OH group;    -   (ii) condensing the product of step (i) with a phosphoramidite        of formula (III), wherein B, R₁, R₅, R_(p) and R are as defined        above, and each B, R₁, R₅, R_(p) and R may be the same or        different from any other B, R₁, R₅, R_(p) and R, respectively;    -   (iii) oxidizing the product of step (ii); and    -   (iv) repeating steps (i)-(iii) n−2 times;        to form the compound of formula (II).

In one embodiment, R₃ is H.

In another embodiment, R₃ is a protecting group, and the process furthercomprises removal of the R₃ protecting group.

In another embodiment of the above processes, the R₃ protecting group isa levulinyl (Lev) group. In yet another embodiment of the aboveprocesses, the R₃ protecting group is an ionic tag linker. In still yetanother embodiment of the above processes, the ionic tag linker isselected from:

wherein X is selected from NH and O.

In another embodiment, when R₃ is

R is selected from lower alkyl, or the N(R)₂ moiety is a cyclicalkylamine, or a substituted cyclic alkylamine, preferably morpholine.

In another embodiment of the above processes:

R₁ is TBDMS;

R₅ is selected from DMTr and MMTr;

R_(p) is selected from methyl (Me), 2-cyanoethyl (CNEt),ortho-chlorophenyl (o-ClPh), and para-chlorophenyl (p-ClPh);

R is selected from isopropyl, methyl, and ethyl; and

B is a nucleobase protected on at least one nitrogen by a suitableN-protecting group,

-   -   wherein the N-protecting group is selected from levulinyl,        acetyl, difluoroacetyl, trifluoroacetyl, isobutyryl, benzoyl,        9-fluorenylmethoxycarbonyl, phenoxyacetyl, dimethylformamidine,        and N,N-diphenyl carbamate.

In another embodiment of the above processes, R₅ is DMTr, R_(p) ismethyl, and R is iPr.

Non limiting examples of the synthesis of the ionic tag linkers andtheir esterification with nucleosides are shown in Schemes 8 and 9. Theionic tag linkers of nucleosides K1, K2 and K3, like the levulinylgroup, require one of the mildest sets of cleavage conditions forselective removal from the other protecting groups used in RNAsynthesis, i.e., a simple treatment with hydrazine hydrate in a pyridineand acetic acid solution. Furthermore, their ionic nature permitsprecipitation based purification of the nucleoside (e.g., compounds (61)or (62), Schemes 8-9), or if desired, di- and tri-nucleotides derivedfrom such ion tagged nucleoside. Scheme 8 depicts a methodology tosynthesize a 2′-deoxynucleoside with a hydrazine cleavable gammaketoester tag, which facilitates isolation via precipitation step.

Upon selective removal of the tag, the nucleoside (or dimer or trimerblock) can be converted into 3′-phosphoramidite derivatives, byprotocols described herein, that may be used in block condensations.

Several approaches can be applied to obtain the required gamma-ketoacid(60). For example, Scheme 8 employs a Stetter reaction as the first step[(51)+(52)→(54)], a reaction that transforms aldehydes into nucleophilesusing catalytic amounts of a thiazolium salt, e.g., (53), in thepresence of a mild base (Stetter, H. Angewandte Chemie, InternationalEdition in English 15: 639-47 (1976)). Thus 4-pentenal (51), an aldehydeattached to an aliphatic chain terminating in an alkene, was activatedas a nucleophile and allowed to undergo a Michael addition using ethylacrylate (52) as the electrophile. The substrates were mixed withthiazolium salt (53) and dissolved in ethanol. The reaction mixture washeated and once it was refluxing gently, the reaction was initiated bythe addition of triethylamine. After 18 hours the solvent was removedand the material obtained was subjected to a dichloromethane/brineextraction followed by flash chromatography. The desired product, (54),co-eluted with an acyloin side-product, (55), in all the solvent systemsinvestigated for the purification. The yield was approximately 25% (asestimated by ¹H-NMR analysis of the mixture), however, enough materialcan readily be obtained to continue with the synthesis, with theimpurity (55) becoming easily separable after the subsequent step. Thenext step in the synthetic route was to protect ketone (54) as an acetal[i.e., (56)]. Refluxing for 4 hours was found to be adequate for thisreaction to reach completion and the desired product (56) was obtainedin 90-95% yield. The product (56) was easily separable from the acyloinside-product (55) generated in the earlier step, which did not appear toundergo any transformation in the acetal formation reaction. Theidentity and purity of (56) were confirmed by TLC, LR-MS and NMR.

With the gamma-acetal-ester, (56), in hand, the next step (Scheme 8) wasthe hydroboration of the terminal alkene. This was achieved using an insitu generated dicyclohexyl borohydride reagent. An appropriate amountof cyclohexene was added to borane-THF at 0° C. and allowed to react forone hour, then (56) was added to the resultant slurry and the reactionwas allowed to proceed for 2 hours at room temperature. The oxidation ofthe intermediate borane was achieved by the addition of aqueous sodiumperborate, a mild oxidant that left the ester intact, and the reactionwas continued for another 2 hours. The reaction mixture was thenextracted with ethyl acetate and the product, (57), was purified byflash column chromatography, providing a colourless liquid in 80-85%yield, with 15-20% of (56) also being recovered. This reaction neverproceeded further than 85% conversion, even with longer reaction timesor an increase in the amount of the borohydride reagent generatedrelative to substrate.

The primary alcohol, (57), was then mixed with triphenylphosphine andtetrabromomethane in DCM in order to generate the terminal bromide (58).The reaction proceeded cleanly but upon aqueous workup, acetal cleavageoccurred, likely due to the formation of hydrobromic acid from thehydrolysis of the excess reagents. The reaction was performed again inthe presence of imidazole, which neutralized any hydrobromic acidgenerated, and the desired product, (58), was obtained in 79-86% yieldafter flash chromatography. Subsequent condensation with1,2-dimethylimidazole in acetonitrile resulted in the ionic tag linker,(59), in 95% or greater yield.

The final steps in the synthesis (Scheme 8) involved the cleavage of theacetal and ester as well as anion metathesis of the ionic moiety andfinally derivatization to a nucleoside. Initially aqueous acid was usedto effectuate the deprotection, followed by anion metathesis but thematerial thus derived decomposed rapidly. Subsequently deprotection wasperformed via a two step process, the first a base mediated cleavage ofthe ester (59) followed by a limited acidification to protonate thecarboxylic acid and cleave the acetal. The protected material, (59), wasthus dissolved in aqueous sodium hydroxide and allowed to react for16-18 hours followed by the addition of aqueous concentrated HCl tobring the solution to approximately pH 1 and finally drying underreduced pressure. The excess salt was removed by suspending theresulting solid in acetonitrile/dichloromethane and filtering off theinsoluble material. The product obtained, (60), appeared pure by TLC,LR-MS and NMR but likely still contained a small amount of sodiumchloride, which could not be detected with these techniques. Anionmetathesis at this point also led to significant decomposition of theresulting product, as in the acid mediated deprotection. The bromidesalt, (60), was stable upon long term storage, however, and was found tocouple in the expected manner with a nucleoside. In fact, usingO-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate(TBTU) as the coupling agent achieved both the coupling and anionexchange simultaneously, with the coupling proceeding quantitatively andthe anion exchange confirmed by LR-MS as an absence of bromide ions andthe presence of tetrafluoroborate in the negative mode. This product(61) was also stable upon long term storage.

With a derivatized nucleoside (61) in hand, the cleavage characteristicsof the orthogonal gamma-ketoester ionic tag linker from the nucleosidewere studied and compared to those of the levulinyl ester protectinggroup, which has been used as described above to generate oligomericbuilding blocks and is known to be easily removed without affecting anyother protecting groups in the molecule. The rate of levulinyl estercleavage under the conditions studied was faster than that of the ionictag linker, with half lives of approximately 0.76 and 2.82 minutesrespectively, corresponding to complete cleavage of the levulinyl esterin just over 5 minutes while the tag required almost 20 minutes for fullcleavage. However, even though the tag cleaves more slowly than thelevulinyl ester under the conditions studied, the normal reaction timeemployed for the cleavage of the 3′-hydroxyl protected levulinyl esterby hydrazine is 20 minutes and no degradation is observed in any of theother protecting groups in that time. This indicated that the ionic taglinker is suitable to the required task, and it is therefore a viableroute to generating oligomeric building blocks as well.

The tag was also condensed with a 5′-O-DMTr-2′-O-TIPS Uridine nucleoside(12) (Scheme 9) using the same conditions employed for thederivatization of 5′-O-DMTr-Thymidine. The ¹H-NMR of the coupledribonucleoside did not appear to show any 2′-3′ silyl isomerisation.

As an alternative to the gamma-ketoester linker 60, a novel linkerderived from ketopemilic acid was developed (Scheme 10).

Its synthesis started by treating ketopemilic acid (63) withiso-propanol and catalytic para-toluenesulfonic acid using a Dean-Starktrap to esterify both terminal carboxylic acid moieties, affording (64).The use of methanol and ethanol (instead of isopropanol) in thisreaction resulted in lactone formation as the major product, instead ofthe desired diester (64).

The diisopropyl ester (64) was isolated and then reacted with ethyleneglycol and catalytic pyridiniumpara-toluenesulfonate by refluxing in aDean Stark trap overnight to form the cyclic ketal (65) in 65% yieldover two steps. Attempts to use ethylene glycol directly to form boththe cyclic ketal and glycol ester resulted in the undesired lactonederivative (Scheme 11), necessitating that esterification and acetalformation be carried out in two separate steps.

Cyclic ketal diester (65) was taken up in methanol and 5 equivalents ofaqueous lithium hydroxide were added to the reaction to preferentiallyhydrolyze one ester over both, producing a mixture of compounds (66) and(67), which were separated in yields of 40 and 60%, respectively.Coupling to the phosphonium ionic tag (68) to the cyclic ketal monoester(67) was accomplished using TBTU and DIPEA in acetonitrile at roomtemperature for 6 h affording compound (69) in 84% yield. Afterisolation the isopropyl ester was hydrolyzed by LiOH in MeOH/Water toafford compound (70) in nearly quantitative yield. If in an alternativemethod, the diisopropyl ester (64) and (65) were not isolated after eachstep, it can be imagined that the conversion of (63) to (66) or (67)could be achieved in one pot.

Also, an alternative approach could be to selectively hydrolyze compound(65) to the di-acid (66), and then couple this material with oneequivalent of the phosphonium tag (68), potentially increasing overallyield and reducing the process by one step.

The ionic tag linker (70) was then conjugated to the 3′-hydroxy ofribonucleoside (12) using standard coupling conditions with TBTU andDIPEA to afford compound (71) in 4 h in a moderate yield of 45%. It isenvisioned that mild acid hydrolysis of (71) would afford K3 (Scheme12).

The ionic tag linker of nucleoside K3 requires mild cleavage conditionsfor removal, that is, treatment with hydrazine hydrate in a pyridine andacetic acid solution. These conditions have been shown to be compatiblewith the protecting groups employed in RNA synthesis. Furthermore, theionic nature of the tag permits precipitation based purification of thenucleoside as carried out for compound (71), or if desired, of di- andtri-nucleotides derived from (71).

Alternatively, given that a tag containing gamma-keto ester isorthogonally cleavable, several other routes to analogous molecules arealso possible. One approach to a similar molecule is shown in Scheme 13,and exploits the 5-bromolevulinyl derived ylid to attach the linker tothe gamma-keto ester moiety as shown in Scheme 13 [Ronald, R. C.;Wheeler, C. J. Journal of Organic Chemistry 48: 138-9 (1983)]. Thiswould also utilize many of the transformations already demonstrated forthe Stetter approach depicted in Scheme 8. Indeed it may even bepossible to link the tag in a single step with this approach, sincecompounds containing the ionic moiety and an aldehyde can be easilyprepared.

The hydrogenation of the resulting alkene would likely be necessarysince it would be conjugated to the ketone and this conjugated systemwould likely react more slowly with hydrazine during the cleavage of thetag. It is understood that other ionic tags may replace thedimethylimidazolium tag shown, such as those described in PCTApplication Publication No. WO 2006/096963 to Chan, T.-H. et al., thecontents of which are incorporated herein by reference in theirentirety. Suitable ionic tags may include, for example, phosphoniumionic tags.

Another possible approach to the same substrate would be to use a moretraditional Umpolung reaction than the Stetter approach, employing adithiane derived from the same aldehydes as the nucleophile (Scheme 14).

The same Michael acceptor could be used and this approach wouldeliminate the competing self-condensation reaction observed in theStetter reaction [Scheme 8, product (55)]. The dithiane would also serveas the ketone protecting group for the bulk of the reaction and wouldlikely be stable to the fluoride treatment employed for removal of thesilyl ether (TBMS). This approach would also use many of thetransformations described herein, though the timing of the dithianecleavage to liberate the ketone might be required prior to theinstallation of the ionic moiety, if the reagents used for this cleavageprove difficult to separate from the desired product. In that case, thedithiane could be cleaved immediately after the carbon-carbon bondformation and an acetal could then be installed.

An alternative to the orthogonal levulinyl linker described above is alight cleavable linker which can be removed in the presence of allstandard ribonucleotide protecting groups. This allows for the use ofextremely mild conditions to expose the 3′-hydroxyl group at anytimeduring the synthesis of blockers. In combination with the 2′-TIPSprotecting group there is no risk of silyl migration, allowing for theproduction of regioisomerically pure blockmers which can be readilyconverted into phosphoramidies. The synthesis of the NPPOC likederivative (80) begins with a few short and elegant steps reported byPfleiderer [Pfleiderer, W. et al. Helvetica Chemimica Acta, 87: 620(2004)].

Fuming nitric acid was cooled to −10° C. and 4-ethylbenzoic acid (72)was added over 30 min to the sitting solution, then allowed to stir for30 min. The mixture was quenched over crushed ice and the solidprecipitate of 3-nitro-4-ethyl-benzoic acid (73) was collected andcrystallised with ethyl acetate and hexanes in good yield (95%). Thetert-butyl ester was formed using DCC and DMAP with tert-butanol understandard conditions.

The formation of the 2-substituted propan-1-ol derivative was achievedas described by Pfleiderer by treating the tert-butyl ester withpara-formaldehyde and a catalytic amount of potassium tert-butoxide inan aprotic dipolar solvent, such as DMF or DMSO, at 90° C. for 3 h[Pfleiderer, W. et al. Helvetica Chemimica Acta, 87: 620 (2004)]. Thereaction is then quenched and neutralized to pH 7 with 1 M HCl, yielding85-90% of the desired product (76). The newly formed primary hydroxyl isthen protected with Fmoc-Cl (77), an acid stable protecting group. Thisallows cleavage of the t-butyl ester with 80% TFA in DCM withoutdeprotection of the primary hydroxyl group. Without Fmoc protection,dehydration of the newly formed hydroxyl will occur, forming the propenederivative. As well, after the installation of the Fmoc it is imperativethat the compound is not exposed to sunlight or tungsten light for longperiods of time, as this compound will undergo photolytic cleavage, asper the design of the molecule.

The newly formed free acid was then coupled with phosphonium ionic tag(53) with TBTU in ACN and wrapped in aluminum foil for 8 h whichafforded the tagged species (79) in a moderate yield of 65%, which canbe easily separated from any starting material by column chromatography.Next, the Fmoc group was removed under standard conditions by treatmentwith 20% 4-methylpiperidine in DMF for 2 h, yielding compound (80) ingood yields. Although no protecting group can be removed at the primaryalcohol, this compound should be kept in the dark at all times. This isdue to the fact that it was observed that some degradation does occurover time, albeit much more slowly than when the Fmoc was present.

The previous synthesis of the light labile linker is somewhat long andrequires the use of an expensive transient protecting group, Fmoc. In anattempt to shorten the synthesis we were able to avoid protection,deprotection, and re-protection of the carboxylic acid moiety, whileincreasing overall yields. This was accomplished by directly conjugatinga modified phosphonium ionic tag (68) containing a primary amine inplace of the hydroxyl group, creating an amide bond in compound (81)(Scheme 16). This was achieved as described for the synthesis of (80)(Scheme 15) using TBTU and triethylamine as coupling reagents, producing(82) in 35% yield (unoptimized).

In another embodiment, there is provided a process for attaching anionic tag linker (82) to a ribonucleoside, affording a building block,(85) or (86), for further elaboration into oligonucleotides. The generalmethod for carrying out the conjugation is shown in Scheme 16, andinvolves phosgenation of an ionic tag linker followed by its attachmentto the 3′-hydroxyl group of a nucleoside.

Thus, phosgenation of (80) or (82) was carried out by a modifiedprocedure from Eckert, H. Auerweck, J. Org. Process Res. Dev. 14:1501-1505, (2010), and is outlined in Scheme 17. Detailed experimentalprocedures for generating phosgene from triphosgene and phenanthridineare described in the Experimental section (Examples).

A solution of nucleoside (12) in acetonitrile was added directly tomixture of DIPEA and the phosgene generated above, and allowed to stirfor 8 h at room temperature. After addition of ethyl acetate, themixture was washed with sat. NaHCO₃ and brine, and precipitated in MTBEto remove excess (unreacted) nucleoside and DIPEA. The resultingprecipitate was further purified by column chromatography in DCM:MeOH.

Nucleosides such as (86) have a number of applications. They can serveas starting materials for the synthesis of dimer or trimers or largeroligonucleotides requiring only a precipitation step for isolation byvirtue of the polar ionic tag linker at the 3′-termini. Once the desiredlength has been synthesized, the 3′-tag and all protecting groups can becleaved yielding the free (unprotected) oligonucleotide. Alternatively,because the 3′-ion tag can be selectively cleaved without deblocking allother protecting group on the heterocylic bases or sugar-phosphatebackbone, it provides a novel means for preparing protectedoligonucleotide blocks containing a 3′-hydroxyl group that can befurther elaborated to a 3′-phosphoramidite derivative.

These processes are exemplified in the synthesis of the tetranucleotiderAGCU starting from nucleoside (86) (Schemes 18 and 19). Reactions werecarried out in the dark by wrapping the reactions flasks with aluminumfoil, to avoid premature cleavage of its ionic photolabile tag.

3′-Tagged-uridine (86) was detritylated by adding 3% trifluoroaceticacid in DCM and allowing the mixture to stir for 5 min. Addition ofmethanol ensured quenching of the trityl cation, preventing there-tritylation of the 5′-hydroxyl group. The crude product was thenprecipitated in MTBE to remove DMTrOMe, and/or DMTrOH. The compound wasthen filtered over celite, collected in DCM and re-purified by columnchromatography affording P4 in 95% yield. The synthesis of dimer rCpU(90) from P4 was carried out by coupling with rC phosphoramidite monomer(88) in the presence of 4,5-dicyanoimidazole (DCI), and the resultingsolution was allowed to stir at room temperature for 3 h. Tenequivalents of tert-butanol was added to quench excess phosphoramidite,followed by 10 eq of tert-butyl hydroperoxide (1 mL of a 6 M solution indecane) to oxidize the internucleotide phosphite triester to the morestable phosphate triester. The reaction was then concentrated to an oil,taken up in minimal amounts of dichloromethane (DCM), and precipitatedin MTBE to remove all excess reagents. The precipitation process wasrepeated if the presence of any quenched phosphoramidite was detected byTLC. Tagged rCU dimer (90) was isolated in 95% yield (0.63 g). The aboveprocess was repeated as described above, using the appropriatephosphoramidites until tetramer (92) was obtained. Full experimentalprocedures and characterization are provided in the Experimental section(Examples).

Tetramer (91) was dissolved in 1 mL of wet ACN (1200 ppm of H₂O), andtransferred into a quartz cuvette. The cuvette was placed inside aphotoreactor with stirring. The reaction was completed within 15 min(TLC analysis). The mixture was concentrated to about half volume andthe cleaved tag removed by precipitation with methyl t-butyl ether(MTBE). The desired tetramer was found in the MTBE solution, which wascollected after concentrating the solution to dryness. Isolated yieldwas 95% (92 mg). Phosphitylation of (92), as described previously, canprovide the 3′-phosphoramidite derivative (93) that is suitable for RNAsynthesis via block coupling.

Oligonucleotide Synthesis

In another embodiment, there is provided a process for preparing anN-mer oligonucleotide, said process comprising:

a) condensing a phosphoramidite of formula (IIa):

-   -   wherein    -   n is an integer from 0 to 19;    -   R₁ is a protecting group;    -   R₅ is a protecting group;    -   R_(p) is a protecting group;    -   R is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine, or        a substituted cyclic alkylamine, preferably morpholine;    -   B is a nitrogen-containing base;    -   wherein each B, R₁ and R_(p) may be the same or different from        any other B, R₁ and R_(p), respectively;    -   with    -   (a′) a functionalized linker L bound to a support

-   -   -   wherein

-   -   is selected from a solid support or an ionic support, or    -   (b′) a compound of formula

-   -   wherein ^((5′-OH))N is a nucleoside/oligonucleotide chain bound        to the solid support or the ionic support via the functionalized        linker L and having a free 5′-OH group;        b) oxidizing the product of step (a) to form a compound of        formula (VIII):

-   -   wherein    -   y is 0 or 1;    -   n, B, R₁, R₅

-   -   R_(p) L, and N are as defined above; and        c) optionally,    -   (i) deprotecting the terminal 5′-OR₅ group of the product of the        previous step to form a free 5′-OH group;    -   (ii) condensing the product of step (i) with a phosphoramidite        of formula (IIa)

-   -   -   wherein n, B, R₁, R₅, R_(p) and R are as defined above, and            each n, B, R₁, R₅, R_(p) and R may be the same or different            from any other n, B, R₁, R₅, R_(p) and R, respectively;

    -   (iii) oxidizing the product of step (ii); and

    -   (iv) optionally repeating steps (i)-(iii);        with the proviso that if y is 0, step (c) is not optional;

to form a bound N-mer oligonucleotide.

In another embodiment, y is 1 and N is a nucleoside.

In yet another embodiment,

In still yet another embodiment, there is provided a process forpreparing an N-mer oligonucleotide, said process comprising:

a) condensing a compound of formula (IIb):

-   -   wherein    -   n is an integer from 0 to 19;    -   R₁ is a protecting group;    -   R₅ is a protecting group;    -   R_(p) is a protecting group;    -   B is a nitrogen-containing base;    -   wherein each B, R₁ and R_(p) may be the same or different from        any other B,    -   R₁ and R_(p), respectively;    -   with    -   a functionalized linker L bound to an ionic support

b) oxidizing the product of step (a) to form a compound of formula (IX):

-   -   wherein    -   n, B, R₁, R₅

-   -   R_(p) and L, are as defined above; and        c) (i) deprotecting the terminal 5′-OR₅ group of the product of        the previous step to form a free 5′-OH group;    -   (ii) condensing the product of step (i) with a phosphoramidite        of formula (IIa)

-   -   -   wherein n, B, R₁, R₅, and R_(p) are as defined above, and R            is lower alkyl, or the N(R)₂ moiety is a cyclic alkylamine,            or a substituted cyclic alkylamine, preferably morpholine;            wherein each n, B, R₁, R₅, and R_(p) may be the same or            different from any other n, B, R₁, R₅, and R_(p),            respectively;

    -   (iii) oxidizing the product of step (ii); and

    -   (iv) optionally repeating steps (i)-(iii);        to form a bound N-mer oligonucleotide.

In another embodiment of the above processes, n is selected from 0, 1,2, or 3.

In yet another embodiment of the above processes:

R₁ is TBDMS;

R₅ is selected from DMTr and MMTr;

R_(p) is selected from methyl (Me), 2-cyanoethyl (CNEt),ortho-chlorophenyl (o-ClPh), and para-chlorophenyl (p-ClPh);

R is selected from isopropyl, methyl, and ethyl; and

B is a nucleobase protected on at least one nitrogen by a suitableN-protecting group,

-   -   wherein the N-protecting group is selected from levulinyl,        acetyl, difluoroacetyl, trifluoroacetyl, isobutyryl, benzoyl,        9-fluorenylmethoxycarbonyl, phenoxyacetyl, dimethylformamidine,        and N,N-diphenyl carbamate.

In still yet another embodiment of the above processes:

R₅ is DMTr;

R_(p) is methyl; and

R is iPr.

In another embodiment of the above processes, the processes furthercomprise fully deprotecting the bound N-mer oligonucleotide to yield afree N-mer oligonucleotide. In another embodiment of the aboveprocesses, the N-mer oligonucleotide has a length from 4-100ribonucleotides. In yet another embodiment of the above processes, theN-mer oligonucleotide has a length from 4-100 deoxyribonucleotides.

In another embodiment of the above processes,

is selected from:

wherein X is selected from NH and O.

In yet another embodiment, there is provided an oligonucleotide preparedby the above processes. In one embodiment, the oligonucleotide preparedby the above processes is an oligoribonucleotide. In another embodiment,the oligonucleotide prepared by the above processes is anoligodeoxyribonucleotide.

Suitable solid supports for use in the above-mentioned processes areknown to those of skill in the art and may include controlled pore glass(CPG) or long chain alkylamine CPG (LCAA-CPG); polystyrene, polyvinyl,and the like.

Suitable ionic supports are also known to those of skill in the art.These may include those described in PCT Application Publication No. WO2006/096963 to Chan, T.-H. et al., the contents of which areincorporated herein by reference in its entirety. Suitable ionicsupports may include, for example, imidazolium and phosphonium ionicsalts.

Functionalized linkers (“L” in formulae (VIII) and (IX)) are usuallyattached to solid/ionic supports to space out the oligomer from thesurface of the support, and suitable linkers are known to those of skillin the art. The most common ones used with CPG (controlled-pore glass)and highly cross-linked polystyrene (PS) solid supports are long-chainalkylamines that are further functionalized with a succinyl, oxalyl,hydroquinone-O,O′-diacetic acid (‘Q-linker’), or universal linkers likethose described in U.S. Pat. No. 6,770,754; European Patent No.:1404695; Guzaev, A. P. et al. J. Am. Chem. Soc., 125, 2380-2381 (2003).Other options for linkers are disclosed in Pon, R. T. et al. NucleicAcids Research, 25, 3629-3635 (1997), the contents of which areincorporated herein by reference in its entirety.

As noted above, the moiety

may be selected from

and orthogonally cleavable ionic tag linkers such as

wherein X is selected from NH and O.

The utility of the dimer and trimer synthons described herein was testedthrough the solution phase synthesis of a decanucleotide,5′-rUUAAUUAA-dTT-3′, and the solid phase synthesis of oligonucleotidesof uridine and mixed uridine/adenosine composition. The decamer wasconstructed by coupling of the previously synthesized dimer amiditeblocks UpU (30) and ApA (47) (shown in Schemes 1 and 6) with a dTpdTdimer attached to a novel tetraalkylphosphonium ion tag (Scheme 21).

In an embodiment, the present invention relates to methods for synthesisof oligomers, including but not limited to oligopeptides,oligosaccharides and oligonucleotides (e.g., oligoribonucleotides,oligodeoxyribonucleotides), in solution using cleavable ionic taglinkers provided herein. In a further embodiment, the present inventionrelates to ionic tag linkers for use in chemical synthesis of oligomers,including but not limited to oligopeptides, oligosaccharides andoligonucleotides, the ionic tag linkers being capable of being cleavableunder conditions which do not cleave other oligomer protecting groups.In an embodiment, the ionic tag linkers are orthogonally cleavable.Ionic tag linkers of the invention are compatible with the varioussynthetic methodologies generally applied in organic synthesis. Morespecifically, ionic tag linkers are compatible with the varioussynthetic methodologies generally applied in the synthesis of oligomers,including but not limited to oligopeptides, oligosaccharides andoligonucleotides (e.g., oligoribonucleotides,oligodeoxyribonucleotides). Furthermore, particularly but notexclusively in the case of oligoribonucleotide synthesis, ionic taglinkers must not induce isomerization of other protecting groups whencleaved. Moreover, solubility of ionic tag linkers is, in an embodiment,not influenced by a growing oligopeptide, oligosaccharide oroligonucleotide chain, such that separation and purification proceduresbecome unduly complex. In an embodiment, separation and purificationprocedures are simplified using ionic tag linkers of the invention, andmay involve washing steps with aqueous and/or organic solvents.

In an embodiment of the present invention, the ionic moiety in an ionictag linker of the invention is an organic salt comprising a heterocyclicor substituted heterocyclic quaternary nitrogen-containing organiccation and an anion balancing the charge on the organic cation. Inanother embodiment an organic cation is selected from the groupconsisting of N-substituted pyridine and 1,3-disubstituted imidazole andthe anion is selected from the group consisting of Cl, Br, BF4, PF6,SbF6, CuCl2, and AICI4. Other ionic moieties are known in the art, andare within the capacity of a skilled technician. Furthermore, it iswithin the capacity of a skilled technician that an anion may also be anorganic anion, non-limiting examples of which include CH₃CO₂, CF₃CO₂,CH₃SO₄, and CF₃SO₂.

In an embodiment, a substrate (reactant) attached to an ionic tag linkeris soluble in polar organic solvents and can undergo liquid-phasereaction. After completion of the reaction and evaporation of thesolvent, excess reagents can be removed by a less polar organic solventin which an ionic tag linker is not soluble. Inorganic reagents and/orside products can be removed by precipitation or by washing with aqueoussolution. A sequence of reactions can be repeated to give more complexstructures. Finally, a product can be detached and then separated froman ionic tag linker by organic solvent extraction. Substrates attachedto an ionic tag linker are expected to largely retain their reactivityanalogously to traditional solution based reactions. Progress ofreactions is readily monitored and analyzed by standard spectroscopictechniques.

In some embodiments, purification of products is achieved simply byprecipitation of an attached ionic tag linker.

In summary, the present invention describes a viable route for thesynthesis of regioisomerically pure dimer and trimer RNAphosphoramidites that couple with similar efficiency as monomericphosphoramidite units. The method increases the overall yield of thetarget oligoribonucleotide sequence by decreasing the number of couplingsteps required for chain assembly and has the potential of significantlysimplifying the final purification of RNA sequences. The presentinvention also demonstrates that dimer and trimer synthons can beutilized either in solution or solid-phase in conjunction with monomersynthons in the final stages of chain assembly, affording n−2 or n−3failure sequences that are more readily resolved. Dimer and trimeramidite blocks will likely find use in the large scale solution (orsolid)-phase synthesis of siRNA drugs. It should be understood thatmethods provided herein are also applicable to DNA synthesis.

In addition, novel solution phase approaches to synthesis ofoligopeptides, oligosaccharides and oligonucleotides, supported by ionictag linkers, are described herein. Ionic tag linkers and methods forlarge scale solution-phase synthesis are provided.

Examples

Diisopropyl 4-oxoheptanedioate (64)

4-ketopemilic acid (63) (10 g, 57.4 mmol; purchased from Sigma-Aldrich)was suspended in 50 mL of isopropanol and 50 mL of benzene. Catalyticamount of p-toluene solfonic acid was added to the mixture and broughtto reflux using a Dean Stark trap to remove the water produced. Once thevolume had decreased to approximately 50 mL in the flask, another 50 mLof 50:50 Benzene:iso-propanol was added and further reduced toapproximately 30 ml. The mixture was then taken up in ethyl acetate andextracted with NaHCO₃ (×3) and once with brine. The organic layer wasdried with MgSO₄ and condensed to dryness yielding pure (64): 14.2 g(95%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 1.06 (d, J=6.45 Hz, 12H) 2.39 (t,J=7.00 Hz, 1H) 2.60 (t, J=6.70 Hz, 4H) 4.72-4.89 (m, 2H)¹³C NMR (75 MHz,CHLOROFORM-d) δ ppm 21.57 (s, 1C) 28.13 (s, 3C) 28.13 (s, 3C) 36.92 (s,3C) 67.66 (s, 1C) 171.90 (s, 2C) 206.82 (s, 1C) C₁₃H₂₂O₅Na¹⁺ lowresolution ESI-MS calculated: 258.14, found: 281.21.

Diisopropyl 3,3′-(1,3-dioxolane-2,2-diyl)dipropanoate (65)

Compound (64) (0.55 g, 2.1 mmol) was solvated with 5 eq of ethyleneglycol (0.58 mL, 10.5 mmol), 90 mL of dry toluene and catalytic amountof pyridinium para-toluene sulfonate. This mixture was refluxed at 140°C. replacing the toluene 3 times and finally allowing the reaction toreflux overnight. The mixture was then distilled to approximately 30 mL,removed from heat and diluted with DCM and extracted with sat. NaHCO₃(×2) then water (×3) to remove any excess ethylene glycol. The productwas purified by column chromatography (DCM:MeOH, 100:0→95:5). Isolatedyield: 0.41 g (65%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.05 (d, J=6.36 Hz, 12H) 1.78 (t,J=7.58 Hz, 15H) 2.16 (t, J=7.58 Hz, 15H) 3.76 (s, 15H) 4.82 (dt,J=12.53, 6.33 Hz, 8H)¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 21.59 (s, 1C)29.02 (s, 1C) 32.07 (s, 1C) 64.94 (s, 1C) 67.23 (s, 1C) 67.26 (s, 1C)109.84 (s, 1C) 172.56 (s, 1C) C₁₅H₂₆O₆Na¹⁺ low resolution ESI-MScalculated: 302.17, found: 325.0.

3-(2-(3-hydroxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanoic acid (66) and3-(2-(3-isopropoxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanoic acid (67)

Compound (65) (1.3 g, 4.3 vmmol) was solvated in 2.5 mL of MeOH to whichwas added 5 eq of LiOH (0.51 g, 21.5 mmol) in 2.5 mL of water. Thismixture was allowed to stir for 6 h until all starting material wasconsumed. The solution was brought to neutrality by the addition of 1 MHCl in MeOH.

This mixture was purified by column chromatography (DCM:MeOH,100:0→90:10). Isolated yield of (66): 0.35 g (40%). Yield of (67): 0.68g (60%).

(66)

¹H NMR (300 MHz, METHANOL-d₄) δ ppm 1.94 (t, J=8.20 Hz, 4H) 2.33 (t,J=7.30 Hz, 15H) 3.94 (s, 26H)¹³C NMR (75 MHz, METHANOL-d₄) δ ppm 28.19(s, 1C) 31.82 (s, 1C) 64.77 (s, 1C) 109.81 (s, 1C) 175.90 (s, 1C)C₉H₁₄O₆Li¹⁻ low resolution ESI-MS calculated: 218.07, found: 224.12.

(67)

¹H NMR (500 MHz, METHANOL-d₄) δ ppm 1.22 (d, J=6.36 Hz, 6H) 1.87-2.03(m, 4H) 2.23-2.34 (m, 4H) 3.55 (m, J=5.14 Hz, 3H) 3.67 (m, J=5.14 Hz,3H) 4.89-5.00 (m, 2H)¹³C NMR (126 MHz, METHANOL-d₄) δ ppm 7.75 (s, 1C)20.72 (s, 1C) 28.80 (s, 1C) 31.81 (s, 1C) 60.87 (s, 1C) 62.94 (s, 1C)67.60 (s, 1C) 72.13 (s, 1C) 109.92 (s, 1C) 173.40 (s, 1C) 176.73 (s, 1C)C₁₂H₂₀O₆ ¹⁻ low resolution ESI-MS calculated: 260.12, found: 259.03.

Tributyl(3-(3-(2-(3-isopropoxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanamido)propyl)phosphoniumbromide (69)

Compound (67) (0.3 g, 1.1 mmol) was solvated in 1.5 mL of ACN followedby TBTU (0.39 g, 1.2 mmol), 2.5 eq of triethylamine (0.38 ml) andphosphonium ionic tag (68) (0.45 g, 1.2 mmol). This mixture was allowedto stir for 4 h until the starting material (67) was completelyconsumed. The reaction mixture was diluted with ethyl acetate andextracted with 5% NaHCO₃×2 and once with brine. The organic layer wasdried and concentrated and purified by column chromatography. DCM:MeOH100:0→95:5. Isolated yield: 0.54 g (84%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=6.74 Hz, 9H) 1.06 (d,J=6.45 Hz, 6H) 1.25 (s, 6H) 1.38-1.59 (m, 11H) 1.80-1.95 (m, 7H)2.15-2.30 (m, 9H) 2.18 (t, J=7.03 Hz, 8H) 3.28-3.44 (m, 2H) 3.84 (br.s., 5H) 3.94 (s, 6H) 4.72-4.89 (m, 1H) C₂₇H₅₃NO₆P¹⁺ low resolutionESI-MS calculated: 502.36, found: 502.36.

Tributyl(3-(3-(2-(3-hydroxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanamido)propyl)phosphonium bromide (70)

Compound (69) (0.25 g, 0.4 mmol) was solvated in 2.5 mL of MeOH to whichwas added 10 eq of LiOH (0.1 g, 4 mmol) in mL of water. This mixture wasallowed to stir for 3 h until all starting material was consumed. Thesolution was brought to neutrality by the addition of 1M HCl in MeOH.This mixture was purified by column chromatography (DCM:MeOH,100:0→90:10). Isolated yield of (70): 0.20 g (95%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=6.74 Hz, 9H) 1.25 (s,6H) 1.38-1.59 (m, 11H) 1.96-2.05 (m, 7H) 2.15-2.30 (m, 9H) 2.40 (t,J=7.03 Hz, 8H) 3.28-3.44 (m, 2H) 3.84 (br. s., 5H) 3.94 (s, 6H)C₂₄H₄₇NO₅P¹⁺ low resolution ESI-MS calculated: 460.31, found: 460.30.

5′-DMTr-2′-TIPS-3′-[tributyl(3-(3-(2-(2-carboxyethyl)-1,3-dioxolan-2-yl)propanamido)propyl)phosphoniumbromide] (71)

To a solution of compound (70) (0.2 g, 0.37 mmol) in ACN (1 mL) wasadded TBTU (0.19 g, 0.6 mmol), triethylamine (0.5 mL) and compound (12)(0.42 g, 0.6 mmol). The resulting mixture was allowed to stir for 12 huntil the starting material (70) was completely consumed. The reactionmixture was diluted with ethyl acetate and extracted with 5% NaHCO₃×2and once with brine. The organic layer was dried and concentrated, takenup in minimal amounts of DCM at precipitated in 100 ml of MTBE, filteredover Celite©. Isolated yield of (71): 0.20 g (45%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=6.74 Hz, 9H) 1.02-1.59(m, 38H) 1.96-2.05 (m, 7H) 2.15-2.30 (m, 9H) 2.40 (t, J=7.03 Hz, 8H)3.37-3.40 (m, 4H) 3.78-3.94 (br. m, 17H) 4.15 (d, J=2.77 Hz, 1H)4.63-4.67 (m, 1H) 5.31 (dd, J=5.14, 2.96 Hz, 1H) 5.40-5.46 (m, 1H) 5.42(s, 1H) 5.99 (d, J=6.32 Hz, 1H) 6.87-6.93 (m, 4H) 7.27-7.37 (m, 7H)7.41-7.45 (m, 2H) 7.75 (d, J=8.30 Hz, 1H) C₆₃H₉₅N₃O₁₂PSi¹⁺ lowresolution ESI-MS calculated: 1144.64, found: 1144.7.

3-Nitro-4-ethyl-benzoic acid (73)

Fuming nitric acid (90%) (150 ml) was cooled with stirring to −10° C.and 4-ethyl benzoic acid (72) (30 g, 0.2 moles; Sigma-Aldrich) was addedslowly over 30 min directly into the sitting solution (1.33 mmol/ml of(72) to fuming nitric acid). The mixture was then allowed to stir for 30min after addition was complete. The mixture was then poured overapproximately 600 g of crushed ice to quench the reaction. The productformed a white ppt which can be filtered over a sintered glass funnel.The excess ice melted by washing the product with water. The sample wasthen re-crystallized from ethyl acetate/hexanes. Two rounds ofcrystallization were preformed. Yield: 37.2 g (95%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.33 (t, J=7.58 Hz, 3H) 2.99 (q,J=7.58 Hz, 2H) 7.52 (d, J=8.07 Hz, 1H) 8.23 (dd, J=8.07, 1.71 Hz, 1H)8.58 (d, J=1.71 Hz, 1H)¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 14.62 (s,1C) 26.38 (s, 1C) 126.37 (s, 1C) 128.29 (s, 1C) 131.67 (s, 1C) 133.87(s, 1C) 144.85 (s, 1C) 149.36 (s, 1C) 170.40 (s, 1C) C₉H₉NO₄Na¹⁺ lowresolution ESI-MS calculated: 195.05, found: 218.2.

tert-Butyl 3-nitro-4-ethyl-benzoate (75)

Compound (73) (19.65 g 0.10 moles) was solvated in 500 ml of THF (0.2 M)followed by 1.15 eq (10.14 g, 0.15 moles) of diisopropylcarbodimide.This mixture was allowed to stir for 5 min followed by 1.5 eq oftert-butanol (17.9 mL) and catalytic amounts of4-(dimethylamino)-pyridine. The mixture was allowed to stir for 60 hbefore the reaction was complete. The reaction was diluted with diethylether and filtered to remove the diisopropylurea (DIU) and condensed todryness. The mixture was solvated in ethyl acetate and extracted with 5%NaHCO₃. The product was separated from (74) by column chromatography(solvent system: hexanes:DCM 100:0→0:100). Yield of (75): 15.1 g (60%);yield of (74): 30%.

(74)

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.94 (d, J=6.45 Hz, 6H) 1.26 (t,J=7.47 Hz, 3H) 1.39 (d, J=6.74 Hz, 6H) 2.91 (q, J=7.33 Hz, 2H) 3.80 (dq,J=13.88, 6.70 Hz, 1H) 4.44 (quin, J=6.74 Hz, 1H) 6.49 (d, J=7.91 Hz, 1H)7.40 (d, J=8.20 Hz, 1H) 7.67 (dd, J=7.91, 1.76 Hz, 1H) 8.02 (d, J=1.76Hz, 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 14.80 (s, 1C) 20.75 (s, 1C)22.04 (s, 1C) 26.12 (s, 1C) 42.96 (s, 1C) 49.54 (s, 1C) 76.63 (s, 1C)77.05 (s, 1C) 77.48 (s, 1C) 123.13 (s, 1C) 130.76 (s, 1C) 131.52 (s, 1C)135.78 (s, 1C) 141.49 (s, 1C) 148.95 (s, 1C) 153.60 (s, 1C) 168.67 (s,1C) C₁₆H₂₃N₃O₄Na¹⁺ low resolution ESI-MS calculated: 321.16, found:344.23.

(75)

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 1.26 (t, J=7.47 Hz, 3H) 1.57 (s,11H) 2.91 (q, J=7.33 Hz, 2H) 7.40 (d, J=7.91 Hz, 1H) 8.08 (dd, J=7.91,1.47 Hz, 1H) 8.38 (d, J=1.47 Hz, 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm14.70 (s, 1C) 26.18 (s, 1C) 28.05 (s, 1C) 76.64 (s, 1C) 77.06 (s, 1C)77.49 (s, 1C) 82.13 (s, 1C) 125.42 (s, 1C) 131.12 (s, 1C) 131.18 (s, 1C)133.23 (s, 1C) 143.00 (s, 1C) 149.12 (s, 1C) 163.56 (s, 1C)C₁₃H₁₇NO₄Na¹⁺ low resolution ESI-MS calculated: 251.11, found: 274.32.

tert-Butyl 4-(1-hydroxypropan-2-yl)-3-nitrobenzoate (76)

Compound (75) (10.5 g, 41.7 mmol) was solvated in 19 mL of DMF (2.2M) towhich 1.5 eq (1.88 g) of paraformaldehyde was added followed by asolution of potassium tert-butoxide (0.12 eq, 0.56 g) in tert-butanol(5.7 mL). This mixture was allowed to stir at room temperature for 10min before being brought up 90° C. for 3 h. The mixture was thenacidified to neutrality by the addition of a 1M HCl monitored by a pHmeter. This mixture was then diluted with sat. NaCl and ethyl acetate(×2). Compound (76) was purified by column chromatography in DCM:ethylacetate 100:0→90:10. Yield: 9.4 g (85%).

¹H NMR (400 MHz, ACETONITRILE-d₃) δ ppm 1.41 (d, J=7.03 Hz, 3H) 3.80(sxt, J=6.88 Hz, 1H) 4.49-4.67 (m, 2H) 7.40 (d, J=7.91 Hz, 1H) 8.08 (dd,J=7.91, 1.47 Hz, 1H) 8.38 (d, J=1.47 Hz, 1H)¹³C NMR (75 MHz,CHLOROFORM-d) δ ppm 17.35 (s, 1C) 27.96 (s, 1C) 36.57 (s, 1C) 67.01 (s,1C) 82.27 (s, 1C) 124.77 (s, 1C) 128.50 (s, 1C) 131.04 (s, 1C) 131.06(s, 1C) 132.81 (s, 1C) 142.62 (s, 1C) 150.41 (s, 1C) 163.58 (s, 1C)C₁₄H₁₉NO₅Na¹⁺ low resolution ESI-MS calculated: 281.12, found: 304.02.

tert-Butyl 4-(1-(F-moc)propan-2-yl)-3-nitrobenzoate (77)

Compound (76) (5.38 g, 20.2 mmol) was co-evaporated with pyridine (×3)and solvated in 97 mL of ACN (0.2M) and 2 eq of pyridine (3.13 mL, 38.7mmol). Fmoc-Cl (5.0 g, 19.33 mmol) was added directly to solution andwas allowed to stir for 16 h in the dark, covered with aluminum foil.The reaction went to completion by TLC. The solution was extracted (×3)with 5% ammonium chloride and once with brine and purified by columnchromatography Hex/EtAc 100:0→75:25. Isolated yield: 8.19 g (86%).

¹H NMR (500 MHz, ACETONITRILE-d₃) δ ppm 1.30 (d, J=7.09 Hz, 3H) 1.60 (s,9H) 3.65 (sxt, J=6.94 Hz, 1H) 4.19 (t, J=6.24 Hz, 1H) 4.23-4.34 (m, 2H)4.39-4.53 (m, 2H) 7.27-7.34 (m, 2H) 7.41 (t, J=7.46 Hz, 2H) 7.53 (d,J=7.34 Hz, 2H) 7.62 (d, J=8.31 Hz, 1H) 7.80 (d, J=7.58 Hz, 2H) 8.13 (dd,J=8.19, 1.59 Hz, 1H) 8.28 (d, J=1.71 Hz, 1H)¹³C NMR (126 MHz,ACETONITRILE-d₃) δ ppm −0.10 (s, 1C) 0.06 (s, 1C) 0.23 (s, 1C) 0.40 (s,1C) 0.56 (s, 1C) 0.73 (s, 1C) 0.89 (s, 1C) 16.83 (s, 1C) 27.30 (s, 1C)27.32 (s, 1C) 33.47 (s, 1C) 46.64 (s, 1C) 68.89 (s, 1C) 70.90 (s, 1C)82.13 (s, 1C) 117.34 (s, 1C) 120.06 (s, 1C) 124.56 (s, 1C) 124.87 (s,1C) 124.90 (s, 1C) 127.17 (s, 1C) 127.18 (s, 1C) 127.81 (s, 1C) 127.83(s, 1C) 128.87 (s, 1C) 131.72 (s, 1C) 132.75 (s, 1C) 141.03 (s, 1C)141.17 (s, 1C) 143.50 (s, 1C) 143.55 (s, 1C) 150.42 (s, 1C) 154.54 (s,1C) 163.26 (s, 1C) C₂₉H₂₉NO₇Na¹⁺ low resolution ESI-MS calculated:503.19, found: 526.41.

4-(1-(Fmoc)propan-2-yl)-3-nitrobenzoic acid (78)

Compound (77) (8.9 g, 17.7 mmol) was directly solvated in a solution of80% TFA in DCM (50 mL) and allowed to stir for 30 min, until allstarting material had been consumed. The sample was then evaporated todryness on the rotovap and purified by column chromatography, Hex/EtAc100:0-60:40. Isolated yield: 6.09 g (77%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.43 (d, J=6.85 Hz, 3H) 3.86 (sxt,J=6.80 Hz, 1H) 4.32-4.46 (m, 4H) 7.28-7.36 (m, 2H) 7.41 (t, J=7.58 Hz,2H) 7.57 (dd, J=6.97, 4.52 Hz, 2H) 7.65 (d, J=8.07 Hz, 1H) 7.76 (d,J=7.34 Hz, 2H) 8.29 (dd, J=8.07, 1.71 Hz, 1H) 8.53 (d, J=1.71 Hz, 1H)11.69 (br. s., 1H)¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 17.58 (s, 1C)33.71 (s, 1C) 46.62 (s, 1C) 70.08 (s, 1C) 71.14 (s, 1C) 76.80 (s, 1C)77.05 (s, 1C) 77.31 (s, 1C) 120.06 (s, 1C) 125.10 (s, 1C) 125.11 (s, 1C)126.16 (s, 1C) 127.16 (s, 1C) 127.17 (s, 1C) 127.91 (s, 1C) 127.93 (s,1C) 128.87 (s, 1C) 129.00 (s, 1C) 133.71 (s, 1C) 141.26 (s, 1C) 141.27(s, 1C) 142.82 (s, 1C) 143.14 (s, 1C) 143.20 (s, 1C) 150.39 (s, 1C)155.00 (s, 1C) 169.79 (s, 1C) C₂₅H₂₀NO₇ ¹⁻ low resolution ESI-MScalculated: 447.13, found: 446.0.

Phosphonium Tag 4-(1-(Fmoc)propan-2-yl)-3-nitrobenzoate (79)

Compound (78) (3.726 g, 8.33 mmol) was solvated in half the solvent(ACN:Py, 28 mL:1.25 mL) to which was added a solution of the phosphoniumtag (53) (3.86 g, 9.16 mmol) in the other half of the solvent, followeddirectly by TBTU (4.0 g, 12.5 mmol). The solution was allowed to stirovernight and by morning the reaction was complete (12 h), and wasconcentrated to half solvent volume then extracted with ethyl acetateand 5% NaHCO₃ (×3) and once with brine. The organic layer was dried withMgSO₄ and condensed to dryness. The compound was then precipitated in500 mL of MTBE to remove the excess pyridine and TBTU byproduct. Theprecipitated white goo was filtered and collected over Celite© thenpurified by column chromatography, DCM:MeOH 100:0→92:8. Isolated yieldof (79): 5.52 g (86%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.81-0.99 (m, 8H) 1.35 (d, J=7.03Hz, 3H) 1.38-1.61 (m, 11H) 1.99-2.38 (m, 8H) 2.66 (br. s., 2H) 3.54-3.83(m, 3H) 4.10-4.41 (m, 5H) 7.21-7.44 (m, 4H) 7.57 (dd, J=10.11, 8.06 Hz,3H) 7.72 (d, J=7.33 Hz, 2H) 8.55 (d, J=1.76 Hz, 1H) 8.70 (dd, J=8.20,1.76 Hz, 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.35 (s, 1C) 17.68 (s,1C) 18.59 (s, 1C) 19.22 (s, 1C) 23.55 (s, 1C) 23.62 (s, 1C) 23.81 (s,1C) 24.01 (s, 1C) 33.40 (s, 1C) 46.62 (s, 1C) 69.91 (s, 1C) 71.36 (s,1C) 76.67 (s, 1C) 77.09 (s, 1C) 77.52 (s, 1C) 119.96 (s, 1C) 124.31 (s,1C) 125.21 (s, 1C) 127.18 (s, 1C) 127.83 (s, 1C) 128.61 (s, 1C) 131.93(s, 1C) 133.41 (s, 1C) 139.59 (s, 1C) 141.19 (s, 1C) 143.27 (s, 1C)143.33 (s, 1C) 150.18 (s, 1C) 154.87 (s, 1C) 165.19 (s, 1C)³¹P NMR (81MHz, CHLOROFORM-d) δ ppm 35.07 (s, 1P) C₄₀H₅₃NO₇P¹⁺ low resolutionESI-MS calculated: 690.30, found: 690.35.

Phosphonium Tag 4-(1-hydroxypropan-2-yl)-3-nitrobenzoate (80)

To compound (79) (6.408 g, 9.29 mmol) was added a 20% solution of4-methylpiperidine in DMF (20 ml). After 2 h the reaction was completeby TLC and the solution was evaporated to dryness, then taken up in DCMand precipitated in 500 ml of MTBE to yield 3.09 g of (80) (71%).

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=7.03 Hz, 11H) 1.26 (d,J=7.03 Hz, 3H) 1.38-1.59 (m, 13H) 1.98 (d, J=7.03 Hz, 2H) 2.11-2.28 (m,7H) 2.36-2.51 (m, 2H) 3.40-3.59 (m, 3H) 3.64-3.82 (m, 2H) 7.51 (d,J=8.21 Hz, 1H) 8.22 (d, J=8.21 Hz, 1H) 8.26 (s, 1H) C₂₅H₄₃NO₅P¹⁺ lowresolution ESI-MS calculated: 468.28, found: 468.28.

Tributyl(3-(4-ethyl-3-nitrobenzamido)propyl)phosphonium bromide (81)

To a solution of 3-nitro-4-ethyl-benzoic acid (73) (3.15 g, 16.1 mmol)and diisopropylethylamine (4 eq, 11.25 ml) in ACN (30 mL) was addedcompound (68) (1.3 eq, 20.9 mmol) and TBTU (1.3 eq, 6.74 g, 20.9 mmol).This mixture was allowed to stir for 12 h. The dark brown solution wasconcentrated to a viscous oil, and taken up in DCM and precipitated in500 ml of MTBE. The solid was collected and re-purified by silica gelcolumn chromatography (DCM:MeOH, 100:0→85:15) eluting as very darkyellow oil. Isolated yield: 7.07 g (84%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 0.90 (t, J=6.97 Hz, 9H) 1.24 (t,J=7.46 Hz, 3H) 1.35-1.56 (m, 12H) 1.96 (d, J=8.07 Hz, 2H) 2.05-2.19 (m,7H) 2.25-2.38 (m, 2H) 2.78 (s, 2H) 2.87 (q, J=7.34 Hz, 2H) 3.60 (q,J=5.79 Hz, 2H) 7.40 (d, J=8.07 Hz, 1H) 7.78 (t, J=5.50 Hz, 1H) 8.07 (d,J=8.07 Hz, 1H) 8.37 (s, 1H) NMR (126 MHz, CHLOROFORM-d) δ ppm 13.21 (s,1C) 14.61 (s, 1C) 18.17 (s, 1C) 18.56 (s, 1C) 23.33 (s, 1C) 23.37 (s,1C) 23.76 (s, 1C) 23.88 (s, 1C) 25.97 (s, 1C) 38.57 (s, 1C) 76.77 (s,1C) 77.02 (s, 1C) 77.28 (s, 1C) 123.82 (s, 1C) 131.09 (s, 1C) 131.47 (s,1C) 132.89 (s, 1C) 141.77 (s, 1C) 149.21 (s, 1C) 165.48 (s, 1C)C₂₄H₄₂N₂O₃P¹⁺ low resolution ESI-MS calculated: 437.29, found: 437.30.

Tributyl(3-(4-(1-hydroxypropan-2-yl)-3-nitrobenzamido)propyl)phosphonium bromide (82)

To a solution of compound (81) (3.56 g, 6.89 mmol) dry DMSO (13.8 mL),was added para-formaldehyde (2.1 eq, 0.43 g, 14.4 mmol). This mixturewas sonicated for 20 min till all of para-formaldehyde dissolved. Theresulting mixture was treated with 1.5 eq of potassium tert-butoxide(1.16 g, 10.3 mmol). The reaction turned a dark purple immediately. Thereaction was allowed to stir for 12 h at room temperature. The reactionwas monitored by MS, showing the disappearance of the starting material.The reaction was treated with 1M HCl in MeOH to bring it to neutralityat which point the reaction was precipitated in diethyl ether, and thenin DCM. This last precipitation step separated the product fromunreacted para-formaldehyde. The product was purified by reverse phasechromatography, using 100 mM TEAA buffer in water (pH 7): ACN80:20-20:80. Isolated yield: 1.3 g (35%).

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.84-0.98 (m, 9H) 1.26 (d, J=7.03Hz, 3H) 1.38-1.59 (m, 11H) 1.98 (d, J=5.86 Hz, 2H) 2.09-2.27 (m, 6H)2.34-2.50 (m, 2H) 3.39-3.49 (m, 1H) 3.53 (d, J=5.47 Hz, 2H) 3.64-3.81(m, 2H) 7.51 (d, J=8.21 Hz, 1H) 8.22 (d, J=8.21 Hz, 1H) 8.26 (s, 1H)8.45 (br. s., 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.38 (s, 1C)17.65 (s, 1C) 18.43 (s, 1C) 19.05 (s, 1C) 23.61 (s, 1C) 23.68 (s, 1C)23.78 (s, 1C) 23.99 (s, 1C) 36.68 (s, 1C) 50.06 (s, 1C) 66.17 (s, 1C)76.69 (s, 1C) 77.11 (s, 1C) 77.54 (s, 1C) 124.73 (s, 1C) 128.38 (s, 1C)129.42 (s, 1C) 133.08 (s, 1C) 144.51 (s, 1C) 150.43 (s, 1C) 164.33 (s,1C)³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 35.07 (s, 1P) C₂₅H₄₄N₂O₄P¹⁺ lowresolution ESI-MS calculated: 467.30, found: 467.31.

5′-DMTr-2′-TIPS-3′-(tributyl(3-(4-(1-hydroxypropan-2-yl)-3-nitrobenzamido)propyl)phosphonium bromide)-uridine (86)

A two necked flask containing the triphosgene and phenanthridine wasconnected to a distillation head and condenser. The receiving end of thecondenser was attached to an ammonia trap and cooled by a dryice/acetone bath to condense the phosgene that was produced. The bottomof the ammonia trap was connected to a three necked round bottom flaskwith a stir bar which was also cooled by a dry ice/acetone bath. Allopen necks of round bottoms were sealed by fresh septa wrapped withTeflon tape. One neck of the three necked flask was punctured with a 20Gneedle attached to a tygon tube and two bubblers in series; the firstwas empty and the second contained mineral oil. Tygon tubing was used toconnect the second bubbler to a 9-inch 20G needle that was fullyinserted into a saturated solution of sodium hydroxide in methanol. Asecond needle and tube was inserted into the septa of the methanolicsodium hydroxide, which acted as a vent up into the fume hood.Triphosgene (1.87 g, 6.33 mmol) and cat. phenanthridine were heated to90° C., at which point the triphosgene melted and solvated thephenanthridine catalyst, promoting the evolution of phosgene gas. After30 min, all triphosgene was consumed and phosgene had begun condensingin the receiving flask. At this point a balloon of argon was puncturedthrough the septa on the two necked flask, pushing any phosgene gas tothe condenser and quenching solution. Once phosgene had stoppedcondensing, an acetonitrile solution of (80) (1.06 g, 1.9 mmol) wasadded dropwise to the stirring phosgene, then removed from the dryice/acetone bath after 10 min. The reaction was stirred for 2 h at roomtemperature. Next, argon gas was passed over the whole apparatus andalso bubbled through the reaction mixture into the methanolic sodiumhydroxide to remove and quench the excess phosgene. NOTE: a very lowflow from a balloon was used at first to ensure the phosgene wasquenched. Once all phosgene was removed, DIPEA (4 mL) was added to themixture to quench the HCl produced in the reaction with phosgene andcompound (82).

A solution of nucleoside (12) (1 eq, 1.35 g, 1.9 mmol) in ACN (3 mL) wasadded directly to the above mixture, and the resulting solution allowedto stir for 8 h at room temperature. The solution was diluted with ethylacetate and extracted with sat. NaHCO₃ (×3) and once with brine. Themixture was precipitated in 300 mL of MTBE to remove excess nucleosideand DIPEA. The resulting precipitate was then purified by columnchromatography (DCM:MeOH 100:0→90:10) to afford 1.32 g of (86) (62%yield).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.82-1.16 (m, 34H) 1.34 (dd,J=6.89, 2.20 Hz, 3H) 1.38-1.63 (m, 15H) 2.05 (br. s., 2H) 2.11-2.31 (m,12H) 2.67 (br. s., 1H) 3.39-3.53 (m, 1H) 3.57-3.72 (m, 3H) 3.78 (s, 7H)4.08-4.38 (m, 2H) 4.59-4.69 (m, 1H) 5.16-5.33 (m, 2H) 5.63-5.76 (m, 1H)6.00 (dd, J=5.27, 2.05 Hz, 1H) 6.81 (dd, J=8.79, 1.47 Hz, 4H) 7.15 (d,J=8.79 Hz, 1H) 7.18-7.41 (m, 10H) 7.56 (d, J=7.91 Hz, 1H) 7.88 (dd,J=8.20, 1.76 Hz, 1H) 8.53 (d, J=7.91 Hz, 1H) 8.67 (t, J=8.94 Hz, 2H)9.64 (br. s., 1H) C₆₅H₉₂N₄O₁₃PSi¹⁺ low resolution ESI-MS calculated:1195.61, found: 1195.60.

Ion-Tagged Synthesis of Tetramer rGACU from Nucleoside (86)

Reactions were carried out in the dark by wrapping the reaction flaskswith aluminum foil.

5′-OH-2′-TIPS-3′-(tributyl(3-(4-(1-hydroxypropan-2-yl)-3-nitrobenzamido)propyl)phosphoniumbromide)-uridine (K3)

3′-Tagged-uridine (86) (0.49 g, 0.38 mmol) was dissolved in 3% TFA inDCM and allowed to stir for 5 min before adding methanol to quench thetrityl cation. The reaction was then concentrated to an oil taken up inminimal amounts of DCM and precipitated in MTBE to removedimethoxytritanol. The compound was filtered over celite, collected inDCM and purified by column chromatography (DCM:MeOH, 100:0→90:10%).Isolated yield of K3: 0.37 g (95%).

¹H NMR (500 MHz, ACETONITRILE-d₃) δ ppm 0.87-1.12 (m, 15H) 1.38 (dd,J=6.97, 3.55 Hz, 1H) 1.42-1.61 (m, 6H) 1.96 (dt, J=4.89, 2.45 Hz, 1H)1.98-2.07 (m, 1H) 2.07-2.17 (m, 3H) 2.22-2.33 (m, 1H) 3.49 (br. s., 1H)3.66-3.79 (m, 1H) 4.13 (dd, J=13.45, 1.96 Hz, 1H) 4.30-4.46 (m, 2H)4.57-4.66 (m, 1H) 5.03 (ddd, J=10.82, 5.07, 1.71 Hz, 1H) 5.70 (d, J=8.07Hz, 1H) 5.85 (dd, J=6.97, 4.28 Hz, 1H) 7.73-7.83 (m, 1H) 8.27 (d, J=8.31Hz, 1H) 8.39 (t, J=1.71 Hz, 1H) 9.17 (br. s., 1H) NMR (126 MHz,ACETONITRILE-d₃) δ ppm −0.16 (s, 1C) 0.17 (s, 1C) 0.34 (s, 1C) 0.36 (s,1C) 0.50 (s, 1C) 0.52 (s, 1C) 0.54 (s, 1C) 0.67 (s, 1C) 0.83 (s, 1C)11.91 (s, 1C) 11.93 (s, 1C) 12.57 (s, 1C) 15.13 (s, 1C) 15.52 (s, 1C)16.93 (s, 1C) 16.99 (s, 1C) 17.00 (s, 1C) 17.01 (s, 1C) 17.11 (s, 1C)17.69 (s, 1C) 18.07 (s, 1C) 20.64 (s, 1C) 20.67 (s, 1C) 22.84 (s, 1C)22.88 (s, 1C) 23.45 (s, 1C) 23.57 (s, 1C) 33.49 (s, 1C) 33.64 (s, 1C)61.34 (s, 1C) 61.37 (s, 1C) 64.62 (s, 1C) 64.76 (s, 1C) 71.11 (s, 1C)71.31 (s, 1C) 73.49 (s, 1C) 76.99 (s, 1C) 77.10 (s, 1C) 82.99 (s, 1C)87.73 (s, 1C) 87.76 (s, 1C) 102.64 (s, 1C) 102.66 (s, 1C) 117.32 (s, 1C)124.83 (s, 1C) 124.86 (s, 1C) 129.10 (s, 1C) 129.32 (s, 1C) 129.84 (s,1C) 129.85 (s, 1C) 133.06 (s, 1C) 133.08 (s, 1C) 140.43 (s, 1C) 140.46(s, 1C) 141.68 (s, 1C) 141.82 (s, 1C) 150.41 (s, 1C) 150.53 (s, 1C)150.81 (s, 1C) 150.83 (s, 1C) 154.10 (s, 1C) 154.15 (s, 1C) 162.65 (s,1C) 164.03 (s, 1C) 164.04 (s, 1C) C₄₄H₇₄N₄O₁₁PSi¹⁺ low resolution ESI-MScalculated: 893.48, found: 893.50.

Synthesis of rCpU (90). Compound K3 (0.37 g, 0.38 mmol) was dried by twoco-evaporations of dry toluene:DCM on a rotovap before placed under highvacuum. K3 was dissolved in 15 ml of ACN containing 2 eq of DCI (0.982g, 8.32 mmol). Immediately after, phoshoramidite (88) (0.51 g 0.57 mmol)was added, and the resulting solution was allowed to stir at roomtemperature for 3 h. MS analysis indicated that the reaction wascomplete (no starting material K3 present). Ten eq of tert-butanol wasadded to quench excess phosphoramidite, followed by 10 eq of tert-butylhydroperoxide (1 mL of a 6 M solution in decane), and the resultingmixture allowed to stir for 20 min until all the phosphite triester wasconverted to the phosphate, as monitored by MS. The reaction was thenconcentrated to an oil, taken up in minimal amounts of DCM, andprecipitated in MTBE to remove all excess reagents. The precipitationprocess was repeated if the presence of any quenched phosphoramidite wasdetected by TLC. Tagged dimer (90) was isolated in 95% yield (0.63 g).C₆₃H₁₂₂N₇O₂₁P₂Si₂ ¹⁺ low resolution ESI-MS calculated: 1670.77, found:1670.73.

The above process was repeated as described above, using the appropriatephosphoramidites till tetramer (92) was obtained. Intermediates isolatedwere characterized (data shown in Table 7 below).

TABLE 7 Characterization of DMTr-rGACU-tag and intermediates StepCompound 5′→3′ Mass cal. (m/z) Mass found (m/z) 1 DMTr-rCU-tag (a)1654.77 1654.71 2 DMTr-rCU-tag (b) (90) 1670.77 1670.73 3 HO-rCU-tag1368.63 1368.59 4 DMTr-rACU-tag (a) 2215.95 1119.46 (M⁺ + Na⁺)/2 5DMTr-rACU-tag (b) 2231.95 1127.44 (M⁺ + Na⁺)/2 6 HO-rACU-tag 1929.821929.80 7 DMTr-rGACU-tag (a) 2645.06 1334.11 (M⁺ + Na⁺)/2 8DMTr-rGACU-tag (b) (91) 2661.05 1341.94 (M⁺ + Na⁺)/2 Tag = light labilephosphonium tag (a) = phosphite triester; (b) = phosphate triester

Photocleavage of Orthogonal Phosphonium Tag from Tetramer (91),Affording Protected DMTr-rGACU-3′OH (92)

Teramer (91) (0.120 g, 0.042 mmol) was dissolved in 1 mL of wet ACN(1200 ppm of H₂O), and transferred into a quartz cuvette (no frostedsides) containing a small stir bar. The cuvette was placed inside aphotoreactor for 15 min with stirring. The reaction appeared complete(TLC analysis). The mixture was concentrated to about half volume andthe cleaved tag precipitated in MTBE (25 mL) and filtered to afford awhite powder. The desired tetramer was found in the MTBE solution, whichwas collected after concentrating the solution to dryness. Isolatedyield: 0.092 g, 0.00403 mmol (95%).

Further Examples

Syntheses of Ionic Tags, for liquid synthesis

where:Y is any cationic atom or organic molecule;X is any anionic atom or organic molecule; andn is any integer from 0 to 10

Several approaches can be applied to obtain the desired gamma-ketoacid(10). For example, Scheme 1 employs a Stetter reaction as the first step[(1)+(2)→(4)], a reaction that transforms aldehydes into nucleophilesusing catalytic amounts of a thiazolium salt, e.g., (3), in the presenceof a mild base (Stetter, H. Angewandte Chemie, International Edition inEnglish 15: 639-47 (1976)). Thus 4-pentenal (1), an aldehyde attached toan aliphatic chain terminating in an alkene, was activated as anucleophile and allowed to undergo a Michael addition using ethylacrylate (2) as the electrophile. The substrates were mixed withthiazolium salt (3) and dissolved in ethanol. The reaction mixture washeated and once it was refluxing gently, the reaction was initiated bythe addition of triethylamine. After 18 hours the solvent was removedand the material obtained was subjected to a dichloromethane/brineextraction followed by flash chromatography. The desired product, (4),co-eluted with an acyloin side-product, (5), in all the solvent systemsinvestigated for the purification. The yield was approximately 25% (asestimated by ¹H-NMR analysis of the mixture), however, enough materialcan readily be obtained to continue with the synthesis, with theimpurity (5) becoming easily separable after the subsequent step. Thenext step in the synthetic route was to protect ketone (4) as an acetal[i.e., (6)]. Refluxing for 4 hours was found to be adequate for thisreaction to reach completion and the desired product (6) was obtained at90-95% yield. The product (6) was easily separable from the acyloinside-product (5) generated in the earlier step, which did not appear toundergo any transformation in the acetal formation reaction. Theidentity and purity of (6) were confirmed by TLC, LR-MS and NMR.

With the gamma-acetal-ester, (6), in hand, the next step (Scheme 22) wasthe hydroboration of the terminal alkene. This was achieved using an insitu generated dicyclohexyl borohydride reagent. An appropriate amountof cyclohexene was added to borane-THF at 0° C. and allowed to react forone hour, then (6) was added to the resultant slurry and the reactionwas allowed to proceed for 2 hours at room temperature. The oxidation ofthe intermediate borane was achieved by the addition of aqueous sodiumperborate, a mild oxidant that left the ester intact, and the reactionwas continued for another 2 hours. The reaction mixture was thenextracted with ethyl acetate and the product, (7), was purified by flashcolumn chromatography, providing a colourless liquid at 80-85% yield,with 15-20% of (6) also being recovered. This reaction never proceededfurther than 85% conversion, even with longer reaction times or anincrease in the amount of the borohydride reagent generated relative tosubstrate.

The primary alcohol, (7), was then mixed with triphenylphosphine andtetrabromomethane in DCM in order to generate the terminal bromide (8).The reaction proceeded cleanly but upon aqueous workup, acetal cleavageoccurred, likely due to the formation of hydrobromic acid from thehydrolysis of the excess reagents. The reaction was performed again inthe presence of imidazole, which neutralized any hydrobromic acidgenerated, and the desired product, (8), was obtained at 79-86% yieldafter flash chromatography. Subsequent condensation with1,2-dimethylimidazole in acetonitrile resulted in the ionic tag, (9), in95% or greater yield.

The final steps in the synthesis (Scheme 1) involved the cleavage of theacetal and ester as well as anion metathesis of the ionic moiety andfinally derivatization to a nucleoside. Initially aqueous acid was usedto effect the deprotection, followed by anion metathesis, but thematerial thus derived decomposed rapidly. Subsequently the deprotectionwas performed via a two step process, the first a base mediated cleavageof the ester (9) followed by a limited acidification to protonate thecarboxylic acid and cleave the acetal. The protected material, (9), wasthus dissolved in aqueous sodium hydroxide and allowed to react for16-18 hours followed by the addition of aqueous concentrated HCl tobring the solution to approximately pH 1 and finally drying underreduced pressure. The excess salt was removed by suspending theresulting solid in acetonitrile/dichloromethane and filtering off theinsoluble material. The product obtained, (10), appeared pure by TLC,LR-MS and NMR but likely still contained a small amount of sodiumchloride, which could not be detected with these techniques. Anionmetathesis at this point also led to significant decomposition of theresulting product, as in the acid mediated deprotection. The bromidesalt, (10), was stable upon long term storage, however, and was found tocouple in the expected manner with a nucleoside. In fact, usingO-(benzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium tetrafluoroborate(TBTU) as the coupling agent achieved both the coupling and anionexchange simultaneously, with the coupling proceeding quantitatively andthe anion exchange confirmed by LR-MS as an absence of bromide ions andthe presence of tetrafluoroborate in the negative mode. This product(12) was also stable upon long term storage.

With a derivatized nucleoside (12) in hand, the cleavage characteristicsof the orthogonal gamma-ketoester ionic tag from the nucleoside werestudied and compared to those of the levulinyl ester protecting group,which has been used as described above to generate oligomeric buildingblocks and is known to be easily removed without affecting any otherprotecting groups in the molecule. The rate of levulinyl ester cleavageunder the conditions studied was faster than that of the ionic tag, withhalf lives of approximately 0.76 and 2.82 minutes respectively,corresponding to complete cleavage of the levulinyl ester in just over 5minutes while the tag required almost 20 minutes for full cleavage.However, even though the tag cleaved more slowly than the levulinylester under the conditions studied, the normal reaction time employedfor the cleavage of the 3′-hydroxyl protected levulinyl ester byhydrazine was 20 minutes and no degradation was observed in any of theother protecting groups in that time. This indicated that the ionic tagis suitable to the required task, and it is therefore a viable route togenerating oligomeric building blocks as well.

The tag was also condensed with a 5′-O-DMTr-2′-O-TIPS Uridine nucleoside(13) (Scheme 2) using the same conditions employed for thederivatization of 5′-O-DMTr-Thymidine. The ¹H-NMR of the coupledribonucleoside did not appear to show any 2′-3′ silyl isomerisation.

To install an alternative ionic tag in place of the imidazolium tagoutlined in scheme 1, the alkyl bromide (8) was simply treated with 1.5eq of tributyl phosphine at 65° C. for 6 h producing the phosphoniumtagged compound (15) quantitatively, which was isolated by precipitationin methyl tert-butyl ether. Unfortunately, the same procedure ofsimultaneous ketal and ester hydrolysis, used in scheme 1, led to theundesired cyclic hemi-lactone (16), and if only the ester was removedand purified, compound (17) was isolated. In either case attempts ofconjugation to a nucleoside (13) as described in scheme 2, using bothTBTU and DCC proved to be difficult, yielding only 5-10% the desirednucleoside conjugate.

The diethyl ketal derivative used in the routes described above is toolabile and allows intermolecular cyclization, inhibiting any coupling toa nucleoside. Thus, a 1,3-dioxolane derivative was used as a more stablederivative. The synthesis (scheme 23) started by treating ketopemilicacid (18) with iso-propanol and catalytic para-toluenesulfonic acidusing a Dean-Stark trap to esterify both terminal carboxylic acidmoieties, affording (19) at 98% yield. The use of methanol and ethanol(instead of isopropanol) in this reaction resulted in lactone formationas the major product, instead of the desired diester (19).

The diisopropyl ester (19) was isolated and then reacted with ethyleneglycol and catalytic pyridiniumpara-toluenesulfonate by refluxing in aDean-Stark trap overnight to form the cyclic ketal (20) in 65% yieldover two steps. Attempts to use ethylene glycol directly to form boththe cyclic ketal and glycol ester resulted in the undesired lactonederivative (Scheme 3), necessitating that esterification and acetalformation be carried out in two separate steps.

Cyclic ketal diester (20) was taken up in methanol and 4 equivalents ofaqueous lithium hydroxide was added to the reaction to preferentiallyhydrolyze one ester over both, producing a mixture of compounds (21) and(22), which were separated in yields of 35% and 45%, respectively.Coupling the phosphonium ionic tag (23) to the cyclic ketal monoester(22) was accomplished using DCC and DMAP in a pyridine/acetonitrilemixture (50:50) at room temperature for 6 h affording the phosphoniumtagged compound (24) in 84% yield. After isolation, the isopropyl esterwas hydrolyzed by LiOH in MeOH/Water to afford compound (25) in nearlyquantitative yield. After column chromatography (MeOH/DCM 0→10% in 1%AcOH) the yield was reduced to 65%, likely due to the phosphonium tag'saffinity to the silica.

The ionically tagged species (25) and NaBr were taken up in methanol toexchange any acetate ion that had exchanged previously during silica gelpurification. If this step were skipped, a significant amount ofacytelated nucleoside formed upon reaction with compound (13). The ionictag (25) was then conjugated to the 3′-hydroxy of ribonucleoside (13)using standard coupling conditions with DCC and DMAP to afford compound(26) in 4 h in a moderate yield of 74%.

Removal of the cyclic ketal was achieved by treatment with either 80%AcOH in water or 5 eq of Pyridiniumnp-tolunesulfonate in 50:50acetone:water at 80° C. over 4 days. The majority of the ketal wasremoved over this time; unfortunately, there was significant removal ofthe TIPS group under these conditions as well. The reaction mixture wasneutralized with saturated sodium bicarbonate and extracted with a brinebicarbonate mixture then columned to yield 38% of the detritylatedcompound (27).

To overcome some of the limitations described above, a thioketal wasused over the traditional cyclic dioxalane approach as shown in Scheme6. Thiophenol and compound (19) were treated with boron trifluorideeitehrate to afford compound (28) in 92% yield. Next, mono hydrolysis ofcompound was achieved by treatment of (28) in MeOH/water (4:1) and with0.2 eq of NaOH at 0° C. drop wise over 30 min. The reaction was allowedto stir at zero for 30 min then the ice bath was removed and thesolution was allowed to warm up to room temperature. The reactionmixture was condensed to remove the methanol and a portion of the water.To the solution was added ethyl acetate and 1M HCl to isolate asignificant amount of starting material and the desired product,compound (30) in 85% yield (in reference to the NaOH added). The abilityto perform HCl workups in this synthetic route was a significantimprovement over using the acyclic and cyclic ketals previously, as thethioketals are much more tolerant to acidic conditions. The phosphoniumionic tag was then conjugated to compound (30) under standard couplingconditions of DCC, DMAP in pyridine:acetonitrile (50:50) to affordcompound (31) in good yield, 87%. Next, the ester of compound (31) washydrolyzed with 5 eq of NaOH in methanol/water to afford compound (32)in near quantitative yield after an HCl extraction in ethyl acetate.

With compound (32) in hand the nucleoside conjugation was achieved,again with the use of DCC and DMAP to afford the nucleoside conjugate(34) in moderate yield. Unfortunately, there was significant byproductformed (33) which could not be completely separated by silica gel columnchromatography. Attempts to reduce the formation of this by the additionof more DMAP, and the use of other coupling reagents, such as TBTU, HATUand CMPI, proved unsuccessful. Conversion of the carboxyl to the acidchloride may be a useful alternative.

The thioketal was then removed by treatment of compound (34) with silvernitrate and molecular iodine in 80% THF/water resulting in a mixture oftritylated and detritylated material. When the same reaction wasattempted in the presence of sodium bicarbonate, a very differentproduct was observed. In this case, the C-5 thiophenyl derivative (35)was formed in moderate yields via electrophilic addition of iodine toC-5 followed by substitution by thiophenol. In another deprotectionstrategy, NBS was used as a source of bromonium ion to cleave thethioketal. Instead, however, bromination of the C-5 position occurred toproduce (36) as the major product. The use of collidine in place ofsodium bicarbonate in the silver nitrate/iodine method reduced theformation of the C-5 thiophenyl derivative to almost nothing. Anothereffective approach that minimized modification at C-5 involved dilutingthe solution of (34) while increasing the amount of silver nitrate andiodine used. The absence of any base produced a mixture of tritylatedand detritylated material, which underwent complete detritylation toafford (27) (Scheme 7).

The material from collidine treated silver nitrate-iodine hydrolysis ofthe thioacetal, compound (37) Scheme 24, was taken and treated with 3%TFA in DCM with 2.5 eq of triethylsilane to quench the trityl cation for10 min, then 20 mL of toluene was added followed by concentration onrotovap. The sample was then taken up in acetone and precipitated frommethyl tert-butyl ether (MTBE) producing an undesired compound (38) in95% yield. This was likely due to the dehydrating conditions created bycondensing the TFA and toluene together. The experiment was repeatedwithout the toluene concentration, but rather a direct precipitationinto MTBE. Similar results were obtained, 60% of compound (38), the restbeing the desired product (27).

Compound (27) derived from the hydrolysis of the thioketal in theabsence of base, which also removed the trityl protecting group, wascoupled with p-methoxy-rU-phosphoramidite (39), followed by oxidation toproduce mainly the undesired dimer nucleotide (41), Scheme 25. Thereaction was monitored by MS, and clearly throughout the reaction theformation of the undesired compound (41) was seen to increase over time.To further identify the reasons for the formation of the enamino esterseen in both compounds (38) and (41), compound (27) was treated with DCIin anhydrous ACN and monitored by MS over time. It was clear after 2 hthat the acidity of DCI was enough to promote the formation of theundesired cyclic enamino product (38).

The inseparable mixture of compound (40) and (41) in Scheme 25 wastreated with 0.5M hydrazine hydrate buffered in pyridine acetic acid(3:2) releasing 8% of the desired UpU dimer (47) isomerically pure.

With the knowledge that acyclic and cyclic acetals are a poor choice fora ketone protecting group on nucleoside conjugates and that keto-gammaamides are not compatible with standard phosphoramidite couplings, analternative synthetic route, scheme 27, was attempted. Compound (15)originally from scheme 3 was taken and the ketal was replaced with thethioketal by treatment with thiophenol and boron trifluoride etherate,producing compound (42) in good yields, 94%. The ester was hydrolysedeasily and quantitatively by sodium hydroxide, and compound (43)isolated by 1M HCl extraction. Unlike with previous attempts, the ketalremained in place and no cyclisation was observed. Coupling to thenucleoside (13) was achieved as previously described in scheme 7,accompanied with the same issue of significant DCC failure product.Despite this small limitation, the synthetic route was continued withoutoptimisation. The thioacetal was removed by silver nitrate/iodine in 80%THF-water followed by detritylation to yield compound (45) in goodyield. Phosphoramidite (39) was coupled to the free 5′-hydroxyl of (45)for 4 h and after the reaction was complete, as monitored by MS, thesample was treated with tert-butanol to couple any excessphosphoramidite and precipitated in MTBE. The sample was then solvatedin DCM then oxidised to yield compound 46 in 96% yield.

An alternative method for producing ionically tagged monomers is shownbelow in Scheme 27B.

Compound (67) was dissolved in dry THF and cooled to 0° C. in an icebath with stirring. To this solution the borane-THF was added drop wiseover 15 min at which point the ice bath was removed and the solution wasstirred at room temperature over 2 h until the reaction was complete.The mixture was once again cooled to 0° C. and methanol was added toquench. The mixture was then concentrated to dryness and treated oncemore with methanol to ensure removal of all trimethyl borate. Thismixture was purified by a column chromatography yielding 95+% of thedesired primary hydroxyl ketal ester (II). Compound (II) was thendissolved in dry DCM and triethylamine, cooled to 0° C. and phosphorustribromide was added drop wise over 10 min and allowed to stir for 1 huntil the reaction was complete as determined by TLC. The mixture wasdiluted with ethyl acetate and extracted twice with saturated sodiumbicarbonate and once with brine, followed by purification by columnchromatography affording the alkyl bromide in good yield of 92%.Compound (III) was dissolved with minimal amounts of acetonitrile towhich tributylphosphine was added drop wise over 10 min. This exothermicreaction was then refluxed for 6 h, concentrated, diluted with minimalacetone and triturated into vigorously stirring hexanes. The hexaneslayer was passed through a Celite® filter and discarded; the remaininggoo on the filter and in the flask was pure phosphonium tagged compound(IV) in quantitative yield. Next, the ketal was replaced with the morestable and more easily removed thioketal by treatment with thiophenoland borane trifluoride etherate in the presence of molecular sieves for6 h at room temperature. This resulted in compound (V) afterpurification by column chromatography in 81% yield. Ester hydrolysis wasperformed with a 0.2M potassium hydroxide solution in a 50:50 water THFmixture. This reaction was quenched by the addition of 1M HCl and sodiumchloride and extracted with ethyl acetate. The organic layer was thenwashed three times with brine to remove any excess HCl, dried andconcentrated providing the pure acid, compound (VI). The nucleoside (13)was coupled to compound (VI) using standard DCC conditions affording the3′ tag-linker nucleoside (VII) in moderate yield of 73%. Lastly thethioketal was removed under very mild conditions by treatment with 20mol % of molecular iodine and in a solution of methanol, water andhydrogen peroxide. This mixture was easily purified by quenching with a10% solution of sodium thiosulfite, extraction with ethyl acetate and ashort silica column, providing the deprotected monomer (VIII) in goodyield of 85%.

Lastly, the dimer nucleotide with the 3′-tag linker (46) was treatedwith hydrazine hydrate (0.5M in pyridine: acetic acid 3:2) producing thedimer nucleotide in near quantitative yield, and the expected linkercleavage product, observed by MS. The dimer nucleotide was isomericallypure as confirmed by phosphorus NMR.

An alternative to the orthogonal levulinyl linker described above is alight cleavable linker which can be removed in the presence of allstandard ribonucleotide protecting groups. This allows for the use ofextremely mild conditions to expose the 3′-hydroxyl group at anytimeduring the synthesis of blockers. In combination with the 2′-TIPSprotecting group there is no risk of silyl migration, allowing for theproduction of regioisomerically pure blockmers which can be readilyconverted into phosphoramidies. The synthesis of the NPPOC likederivative (55) begins with a few short and elegant steps reported byPfleiderer [Pfleiderer, W. et al. Helvetica Chemimica Acta, 87: 620(2004)].

Fuming nitric acid was cooled to −10° C. and 4-ethylbenzoic acid (49)was added over 30 min to the sitting solution, then allowed to stir for30 min. The mixture was quenched over crushed ice and the solidprecipitate of 3-nitro-4-ethyl-benzoic acid (50) was collected andcrystallised with ethyl acetate and hexanes in good yield (95%). Thetert-butyl ester was formed using DCC and DMAP with tert-butanol understandard conditions.

The formation of the 2-substituted propan-1-ol derivative was achievedas described by Pfleiderer by treating the tert-butyl ester withpara-formaldehyde and a catalytic amount of potassium tert-butoxide inan aprotic dipolar solvent, such as DMF or DMSO, at 90° C. for 3 h[Pfleiderer, W. et al. Helvetica Chemimica Acta, 87: 620 (2004)]. Thereaction was then quenched and neutralized to pH 7 with 1 M HCl,yielding 85-90% of the desired product (51). The newly formed primaryhydroxyl was then protected with Fmoc-Cl (52), an acid stable protectinggroup. This allows cleavage of the t-butyl ester with 80% TFA in DCMwithout deprotection of the primary hydroxyl group. Without Fmocprotection, dehydration of the newly formed hydroxyl will occur, formingthe propene derivative. As well, after the installation of the Fmoc itis imperative that the compound is not exposed to sunlight or tungstenlight for long periods of time, as this compound will undergo photolyticcleavage, as per the design of the molecule.

The newly formed free acid was then coupled with phosphonium ionic tag(53) with TBTU in ACN and wrapped in aluminum foil for 8 h which affordsthe tagged species (54) in a moderate yield of 65%, which could beeasily separated from any starting material by column chromatography.Next, the Fmoc group was removed under standard conditions by treatmentwith 20% 4-methylpiperidine in DMF for 2 h, yielding compound (55) ingood yields. Although no protecting group can be removed at the primaryalcohol, this compound should be kept in the dark at all times. This isdue to the fact that it was observed that some degradation does occurover time, albeit much more slowly than when the Fmoc was present.

The previous synthesis of the light labile linker is somewhat long andrequires the use of an expensive transient protecting group, Fmoc. In anattempt to shorten the synthesis, we were able to avoid protection,deprotection, and re-protection of the carboxylic acid moiety, whileincreasing overall yields. This was accomplished by directly conjugatinga modified phosphonium ionic tag (23) containing a primary amine inplace of the hydroxyl group, creating an amide bond in compound (56)(Scheme 30). This was achieved as described for the synthesis of (55)(Scheme 29) using TBTU and triethylamine as coupling reagents, producing(57) in 35% yield (unoptimized).

In another embodiment, there is provided a process for attaching ionictag (57) to a ribonucleoside, affording a building block, (58) or (59),for further elaboration into oligonucleotides. The general method forcarrying out the conjugation is shown in Scheme 31, and involvesphosgenation of the ionic tag followed by its attachment to the3′-hydroxyl group of the nucleoside.

Thus, phosgenation of (55) or (57) was carried out by a modifiedprocedure from Eckert, H. Auerweck, J. Org. Process Res. Dev. 14:1501-1505, (2010), and is outlined in Scheme 32. Detailed experimentalprocedures for generating phosgene from triphosgene and phenanthridineare described herein.

A solution of nucleoside (13) in acetonitrile was added directly tomixture of DIPEA and chloro carbonate produced from the phosgenereaction generated above, and allowed to stir for 8 h at roomtemperature. After addition of ethyl acetate, the mixture was washedwith sat. NaHCO₃ and brine, and precipitated in MTBE to remove excess(unreacted) nucleoside and DIPEA. The resulting precipitate was furtherpurified by column chromatography in DCM:MeOH.

Nucleosides such as (59) have a number of applications. They can serveas starting materials for the synthesis of dimer or trimers or largeroligonucleotides requiring only a precipitation step for isolation byvirtue of the polar ionic tag at the 3′-termini. Once the desired lengthhas been synthesized, the 3′-tag and all protecting groups can becleaved yielding the free (unprotected) oligonucleotide. Alternatively,because the 3′-ion tag can be selectively cleaved without deblocking allother protecting group on the heterocylic bases or sugar-phosphatebackbone, it provides a novel means for preparing protectedoligonucleotide blocks containing a 3′-hydroxyl group that can befurther elaborated to a 3′-phosphoramidite derivative.

3′-NPPOC-tagged-uridine (86) was detritylated by adding 3%trifluoroacetic acid in DCM and triethylsilane, allowing the mixture tostir for 5 min. Addition of methanol ensured quenching of the tritylcation, preventing the re-tritylation of the 5′-hydroxyl group. Thecrude product was then precipitated in MTBE to remove DMTrOMe, and/orDMTrOH. The compound was then filtered over celite, collected in DCM andre-purified by column chromatography affording a 95% yield. Thesynthesis of dimer rUpU (60) was carried out by coupling with rUphosphoramidite monomer (39) in the presence of 4,5-dicyanoimidazole(DCI), and the resulting solution was allowed to stir at roomtemperature for 3 h. Ten equivalents of tert-butanol were added toquench excess phosphoramidite, followed by 10 eq of tert-butylhydroperoxide (1 mL of a 6 M solution in decane) to oxidize theinternucleotide phosphite triester to the more stable phosphatetriester. The reaction was then concentrated to an oil, taken up inminimal amounts of dichloromethane (DCM), and precipitated in MTBE toremove all excess reagents. The precipitation process was repeated ifthe presence of any quenched phosphoramidite was detected by TLC. TaggedrUpU dimer (60) was isolated in 95% yield.

Dimer (60) was dissolved in wet ACN (3200 ppm of H₂O), in a 50 ml Pyrexround bottomed flask. The flask was placed inside a photoreactorequipped with UVB bulbs and reacted for 35 min with stirring at aconcentration of 0.01M. The mixture was concentrated to about 3 ml andthe cleaved tag removed by precipitation with methyl t-butyl ether(MTBE). The desired dimer was found in the MTBE solution, which wascollected after concentrating the solution to dryness. Isolated yieldwas 95%.

Experimental Synthesis of Orthogonally Cleavable Tags

Ethyl 4-oxooct-7-enoate (54)

4-Pentenal (1) (3.8 g, 45 mmol) was mixed with3-benzyl-5-(2-hydroxyethyl)-4-methylthiazolium chloride ((3), 2.45 g,9.1 mmol) and ethyl acrylate ((2), 9.0 g, 90 mmol) and dissolved in 22mL of anhydrous ethanol. The reaction mixture was heated to reflux andthen triethylamine (7.6 mL) was added to begin the reaction. Thereaction mixture was refluxed for 18 hours and was then cooled to roomtemperature. The ethanol was removed under reduced pressure and thereaction mixture was then suspended in dichloromethane and extractedwith brine. The organic layer was dried over magnesium sulphate and thesolvent was removed under reduced pressure. The products were purifiedby flash column chromatography using a hexanes/ethyl acetate gradientelution system to give (4) (3.96 g, mixed with (5), app. 25% yield) as apale yellow oil. ¹H NMR (300 MHz, Acetonitrile-d₃) 8=5.99-5.73 (m, 1H,with acyloin impurity), 5.15-5.05 (m, 2H), 5.04-4.93 (acyloin impurity),4.15-4.06 (q, J=7.0 Hz, 2H), 2.76-2.67 (m, 2H, with acyloin impurity),2.67-2.60 (acyloin impurity), 2.55-2.48 (m, 2H, with acyloin impurity),2.35-2.26 (m, 2H), 2.20-2.17 (acyloin impurity), 2.16-2.12 (m, 2H),1.99-1.94 (acyloin impurity), 1.21 (t, J=7.0 Hz, 3H), C₁₀H₁₆O₃Na¹⁺ lowresolution ESI-MS calculated: 207.10, found: 207.31.

Ethyl 4,4-diethoxyoct-7-enoate (56)

Compound (4) (2.0 g, as mixture with (5), approx. 5.7 mmol) wasdissolved in a 1:1 v/v mixture of ethyl orthoformate and ethanol (6 mL)and mixed with a catalytic amount of pTSA (0.1 g). The reaction mixturewas then refluxed for 4 hours and it was then cooled to 0° C. Saturatedaqueous sodium bicarbonate (20 mL) was then added along with diethylether (20 mL). The aqueous phase was extracted several times withdiethyl ether and then the combined organic layers were rinsed withaqueous brine and dried over magnesium sulphate. The solvent was removedunder reduced pressure and the product was purified by flash columnchromatography using a hexanes/ethyl acetate gradient system to give (6)(1.36 g, 92% yield) as a colourless oil. ¹H NMR (500 MHz, DMSO-d₆)δ=5.85-5.73 (m, 1H), 5.05-4.88 (m, 2H), 4.03 (q, J=7.2 Hz, 2H), 3.32 (q,J=7.0 Hz, 4H), 2.20 (t, J=7.8 Hz, 2H), 1.97-1.88 (m, 2H), 1.79 (t, J=7.8Hz, 2H), 1.53 (t, J=8.4 Hz, 2H), 1.16 (t, J=7.2 Hz, 3H), 1.06 (t, J=7.0Hz, 6H), ¹³C NMR (75 MHz, Acetonitrile-d₃) δ=173.0, 138.5, 113.8, 102.0,60.1, 55.0, 32.3, 28.7, 28.3, 27.8, 14.6, 13.6, C₁₄H₂₆O₄Na¹⁺ lowresolution ESI-MS calculated: 281.17, found: 281.13.

Ethyl 4,4-diethoxy-8-hydroxyoctanoate (7)

A 1 M solution of borane in THF (2.4 mL, 2.4 mmol) was cooled to 0° C.and to it was added, dropwise, 0.47 mL of cyclohexene (4.6 mmol). Thereaction was stirred for 1 hour at 0° C. and to the resultant whiteslurry was added compound (6) (0.51 g, 2.0 mmol). The reaction wasallowed to warm to room temperature and was stirred for 2 hours. Afterthis time, sodium perborate tetrahydrate (1.07 g, 7.0 mmol) and 2.4 mLof water were added. The reaction was stirred for a further 2 hours andthen the reaction mixture was extracted with ethyl acetate severaltimes. The combined organic layers were dried of magnesium sulphate andthe solvent was removed under reduced pressure. The products werepurified using a dichloromethane/methanol gradient elution system togive (7) (0.45 g, 81% yield) as a colourless oil. Starting material (6)was also recovered. ¹H NMR (300 MHz, DMSO-d₆) δ=4.33 (t, J=5.2 Hz, 1H),4.02 (q, J=7.1 Hz, 2H), 3.36 (m, 2H), 3.31 (q, J=7.3 Hz, 4H), 2.18 (t,J=7.7 Hz, 2H), 1.76 (t, J=7.7 Hz, 2H), 1.46-1.41 (m, 2H), 1.40-1.31 (m,2H), 1.25-1.19 (m, 2H), 1.16 (t, J=7.1 Hz, 3H), 1.05 (t, J=7.3 Hz, 6H),¹³C NMR (75 MHz, DMSO-d₆) δ=173.1, 102.4, 61.0, 60.3, 55.0, 33.2, 33.0,29.0, 28.5, 20.2, 15.7, 14.5, C₁₄H₂₈O₅Na¹⁺ low resolution ESI-MScalculated: 299.18, found: 299.19.

Ethyl 8-bromo-4,4-diethoxyoctanoate (8)

Compound (7) (0.50 g, 1.8 mmol) was mixed with triphenylphosphine (0.80g, 3.0 mmol) and imidazole (0.20 g, 2.9 mmol) and dissolved in 18 mL ofdichloromethane. The solution was cooled to 0° C. and a solution ofcarbon tetrabromide (0.85 g, 2.6 mmol) in dichloromethane (1.5 mL) wasadded slowly. The reaction mixture was allowed to warm to roomtemperature and was stirred for 1 hour. The reaction was then quenchedby the addition of saturated aqueous sodium sulphite and extracted withdichloromethane. The combined organic layers were dried over sodiumsulphate and the solvent was removed under reduced pressure. The productwas purified by flash column chromatography with a hexanes/ethyl acetategradient elution system to yield (58) (0.49 g, 81% yield) as acolourless oil. ¹H NMR (400 MHz, DMSO-d₆) δ=4.04 (q, J=7.1 Hz, 2H), 3.54(t, J=6.5 Hz, 2H), 3.32 (q, J=6.9 Hz, 4H), 2.22 (t, J=7.8 Hz, 2H),1.83-1.74 (m, 4H), 1.47 (t, J=7.2 Hz, 2H), 1.35-1.25 (m, 2H), 1.18 (t,J=7.1 Hz, 3H), 1.07 (t, J=6.9 Hz), ¹³C NMR (126 MHz, Acetonitrile-d₃)δ=173.0, 102.1, 60.1, 55.0, 34.2, 32.5, 32.1, 28.8, 28.4, 22.0, 14.7,13.5, C₁₄H₂₇BrO₄Na¹⁺ low resolution ESI-MS calculated: 361.10, found:361.11.

Ethyl 4,4-diethoxy-8-(2,3-dimethyl-1H-imidazol-1-yl) octanoate bromide(9)

Compound 58) (0.31 g, 0.90 mmol) was dissolved in 5 mL of acetonitrileand mixed with 1,2-dimethylimidazole (0.13 g, 1.3 mmol). The reactionwas warmed to 50° C. and stirred overnight. The reaction mixture wasthen cooled to room temperature and the solvent was then removed underreduced pressure. The resultant oil was rinsed several times withdiethyl ether and then the compound was again subjected to reducedpressure. This gave (9) (0.38 g, 95% yield) as a colourless oil. ¹H NMR(500 MHz, DMSO-d₆) δ=7.63 (d, J=2.2 Hz, 1H), 7.60 (d, J=2.2 Hz, 1H),4.09 (t, J=7.2 Hz, 2H), 4.04 (q, J=7.2 Hz, 2H), 3.73 (s, 3H), 3.31 (q,J=6.9 Hz, 4H), 2.56 (s, 3H), 2.20 (t, J=8.1 Hz, 2H), 1.76 (t, J=8.1 Hz,2H), 1.71-1.63 (m, 2H), 1.49 (t, J=7.6 Hz, 2H), 1.24-1.19 (m, 2H), 1.16(t, J=7.2 Hz, 3H), 1.05 (t, J=6.9 Hz, 6H), ¹³C NMR (126 MHz, DMSO-d₆)δ=173.6, 122.8, 121.3, 102.5, 60.7, 55.6, 48.6, 35.3, 33.2, 29.9, 29.3,28.8, 20.8, 15.2, 14.1, 9.7, C₁₉H₃₅N₂O₄ ¹⁺ low resolution ESI-MScalculated: 355.26, found: 355.28.

8-(2,3-dimethyl-1H-imidazol-1-yl)-4-oxooctanoic acid bromide (10)

Compound (9) (0.44 g, 1.0 mmol) was mixed with 1 M aqueous sodiumhydroxide (5 mL) and stirred overnight. The solution was then acidifiedto pH 1 by addition of concentrated aqueous HCl. The aqueous solutionwas then rinsed with diethyl ether, followed by the removal of waterunder reduced pressure. The resulting solid was dissolved in a minimumof cold acetone and dichloromethane any undissolved material was removedby filtration. The solvent was then removed under reduced pressure togive (10) (0.34 g, >100% yield) as an off-white solid, likely mixed witha small amount of sodium chloride. ¹H NMR (400 MHz, DMSO-d₆) δ=7.63 (d,J=2.1 Hz, 1H), 7.61 (d, J=2.1 Hz, 1H), 4.09 (t, J=7.3 Hz, 2H), 3.73 (s,3H), 2.61 (t, J=6.3 Hz, 2H), 2.56 (s, 3H), 2.49 (t, J=7.3 Hz, 2H), 2.37(t, J=6.3 Hz, 2H), 1.65 (m, 2H,), 1.43 (m, 2H), ¹³C NMR (126 MHz,Acetonitrile-d₃) d=208.9, 173.4, 122.3, 120.9, 48.0, 41.0, 36.7, 34.8,28.6, 27.7, 19.9, 9.2, C₁₃H₂₁N₂O₃ ¹⁺ high resolution ESI-MS required:253.15467, found: 253.15459.

General Procedure for the Derivatization of (10) with Nucleosides

Compound (10) (0.4 mmol) was dissolved in 15% v/v DMF/acetonitrile andmixed with DCC (0.6 mmol), DMAP (0.2 mmol), and the desired 5′-DMTr-dTor 5′-DMTr 2′-TIPS rU (13) (0.5 mmol). The reaction mixture was stirredovernight and was then precipitated from MTBE. The resultant solid wasremoved by filtration and recovered from the filter by dissolving it inacetonitrile. The solvent was removed under reduced pressure and theresulting solid was taken up in dichloromethane and washed with diluteaqueous sodium tetrafluoroborate to achieve ion metathesis. The organicphase was dried over magnesium sulphate and the solvent was removedunder reduced pressure. The resultant solid was then dissolved inacetonitrile and the solution was precipitated from MTBE, followed byfiltration and recovery in acetonitrile. The solvent was then removedunder reduced pressure to yield the desired tagged nucleoside in 80-90%yield.

(12)¹H NMR (500 MHz, DMSO-d₆) δ=11.37 (s, 1H), 7.59 (d, J=2.1 Hz, 1H),7.57 (d, J=2.1 Hz, 1H), 7.49 (s, 1H), 7.39-7.36 (m, 2H), 7.34-7.30 (m,2H), 7.29 (t, J=7.1 Hz, 2H), 7.25-7.19 (m, 5H), 6.90-6.85 (m, 4H), 6.17(dd, J=5.9 Hz, 1H), 5.25 (d, J=6.3 Hz, 1H), 4.08 (t, J=7.1 Hz, 2H), 4.01(dd, J=3.5 Hz, 1H), 3.72 (s, 6H), 3.71 (s, 3H), 3.33-3.27 (m, 1H, andH₂O), 3.22-3.17 (dd, J=7.2, 3.3 Hz, 1H), 2.69 (t, J=6.1 Hz, 2H), 2.60(s, 3H), 2.55-2.44 (m, 8H, and DMSO), 2.53 (dd, J=8.1, 5.4 Hz, 1H),1.72-1.61 (m, 2H), 1.48-1.42 (m, 2H), C₄₄H₅₁N₄O₉ ¹⁺ high resolutionESI-MS required: 779.36506, found: 779.36526.

(14)¹H NMR (500 MHz, DMSO-d₆) δ=11.47 (s, 1H, H3), 8.22-8.16 (m, 1H,DMT), 7.72-7.70 (br. s, 1H, H₆), 7.69-7.68 (m, 1H, tag CH═CH), 7.63-7.60(m, 1H, tag CH═CH), 7.60-7.58 (m, 2H, DMTr), 7.58-7.56 (m, 2H, DMTr),7.36-7.27 (m, 2H, DMT), 7.26-7.18 (m, 2H, DMT), 6.91-6.84 (m, 4H, DMTr),5.87 (d, J=6.8 Hz, 1H, H1′), 5.49 (dd, J=2.0, 5.9 Hz, 1H, H5), 5.16 (t,J=2.3 Hz, 1H, H3′), 4.64 (t, J=6.2 Hz, 1H, H2′), 4.06 (t, J=7.4 Hz, 2H,NCH₂), 3.73 (s, 6H, DMT OCH₃), 3.70 (s, 3H, tag NCH₃), 3.29-3.15 (m,water and H5′&5″), 2.70 (t, J=6.7 Hz, 2H, tag CH₂CH₂COO), 2.63-2.58 (m,3H, tag CH₃CN₂), 2.55 (m, DMSO and tag CH₂CH₂COO and tag NCH₂CH₂CH₂CH₂),2.54-2.45 (m, 5H), 1.73-1.61 (m, tag NCH₂CH₂CH₂CH₂ and 10% impurity),1.49-1.35 (m, tag, NCH₂CH₂CH₂CH₂ and 10% impurity), 1.28-1.13 (m,impurity), 0.99-0.90 (m, 9H), C₅₂H₆₉N₄O₁₀Si¹⁺ high resolution ESI-MSrequired: 937.47775, found: 937.47680.

tributyl(5,5,8-triethoxy-8-oxooctyl)phosphonium bromide (15)

Alkyl-bromide (8) (3.8 g, 11.2 mmol) was solvated in 22.4 mL of dry ACNto which was added to 1.5 eq of tributylphosphine (3.4 g, 16.8 mmol) andwas stirred at 50° C. for 8 h. The reaction mixture was thenconcentrated to dryness on rotovap then precipitated in hexanes toafford pure phosphonium tagged species (15) in 93% yield, 5.64 g.

1H NMR (300 MHz, CHLOROFORM-d) □□ ppm 0.76-0.91 (m, 16H) 0.95-1.07 (m,10H) 1.08-1.19 (m, 6H) 1.27-1.58 (m, 33H) 1.71-1.89 (m, 3H) 2.07-2.21(m, 4H) 2.22-2.49 (m, 15H) 3.18-3.39 (m, 8H) 3.88-4.08 (m, 2H) 31P NMR(81 MHz, CHLOROFORM-d) □ ppm 49.63 (s, 1P).

tributyl(4-(2-hydroxy-5-oxotetrahydrofuran-2-yl)butyl)phosphoniumbromide (16)

Compound (15) (0.2 g, 0.37 mmol) was solvated in minimal methanolapprox. 3 mL to which was added 3 mL of 5M HCl and was allowed to stirfor 20 min, at which point the reaction was observed to be complete byTLC. The reaction was then neutralized by the addition of 3 mL of 5MNaOH, then approximately 5 eq (75 mg, 1.9 mmol) of extra NaOH was addedand allowed to stir for an additional 30 min. The reaction was monitoredby MS, showing complete consumption of starting material. The reactionwas then neutralized with 1M HCl, taken up in ethylacetate and shakenacidified brine to remove all excess salts, and twice with brine toremove any excess HCl. The ethyl acetate was dried with magnesiumsulfate and concentrated to dryness. Yielding compound (16) in 88%yield, 176 mg.

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.78-0.97 (m, 9H) 1.45 (br. s.,17H) 1.87 (br. s., 1H) 1.97-2.07 (m, 1H) 2.13 (m, J=9.38, 6.74 Hz, 1H)2.28 (br. s., 8H) 2.38-2.72 (m, 2H) 3.40-3.57 (m, 1H).

tributyl(4-(2-ethoxy-5-oxotetrahydrofuran-2-yl)butyl)phosphonium bromide(17)

Compound (15) (0.25 g, 0.46 mmol) was solvated in minimal amount ofmethanol, 1.5 mL, and treated with approximately 5 eq (80 mg, 2.1 mmol)of NaOH and allowed to stir for 1 h at room temperature. The reactionmixture was neutralized to pH 8 then concentrated to dryness. Themixture was then passed through a silica column with 1% acetic acid and10% MeOH-DCM to remove all salts and generate the acid form of theproduct. Yielding 74% of compound (17).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.78-0.97 (m, 9H) 1.07 (t, J=7.00Hz, 4H) 1.45 (br. s., 17H) 1.87 (br. s., 1H) 1.97-2.07 (m, 1H) 2.13 (m,J=9.38, 6.74 Hz, 1H) 2.28 (br. s., 8H) 2.38-2.72 (m, 2H) 3.23-3.39 (m,2H) 3.40-3.57 (m, 1H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.41 (s, 1C) 15.28 (s, 1C) 18.38(s, 1C) 19.02 (s, 1C) 23.55 (s, 1C) 23.61 (s, 1C) 23.69 (s, 1C) 23.77(s, 1C) 23.97 (s, 1C) 28.70 (s, 1C) 31.54 (s, 1C) 32.59 (s, 1C) 35.21(s, 1C) 42.36 (s, 1C) 55.17 (s, 1C) 57.98 (s, 1C) 102.33 (s, 1C) 110.85(s, 1C) 176.42 (s, 1C) 177.15 (s, 1C).

Diisopropyl 4-oxoheptanedioate (19)

4-ketopemilic acid (18) (10 g, 57.4 mmol; purchased from Sigma-Aldrich)was suspended in 50 mL of isopropanol and 50 mL of benzene. Catalyticamount of p-toluene solfonic acid was added to the mixture and broughtto reflux using a Dean Stark trap to remove the water produced. Once thevolume had decreased to approximately 50 mL in the flask, another 50 mLof 50:50 Benzene:iso-propanol was added and further reduced toapproximately 30 ml. The mixture was then taken up in ethyl acetate andextracted with NaHCO₃ (×3) and once with brine. The organic layer wasdried with MgSO₄ and condensed to dryness yielding pure (19): 14.2 g(95%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 1.06 (d, J=6.45 Hz, 12H) 2.39 (t,J=7.00 Hz, 1H) 2.60 (t, J=6.70 Hz, 4H) 4.72-4.89 (m, 2H)¹³C NMR (75 MHz,CHLOROFORM-d) δ ppm 21.57 (s, 1C) 28.13 (s, 3C) 28.13 (s, 3C) 36.92 (s,3C) 67.66 (s, 1C) 171.90 (s, 2C) 206.82 (s, 1C) C₁₃H₂₂O₅Na¹⁺ lowresolution ESI-MS calculated: 258.14, found: 281.21.

Diisopropyl 3,3′-(1,3-dioxolane-2,2-diyl)dipropanoate (20)

Compound (19) (0.55 g, 2.1 mmol) was solvated with 5 eq of ethyleneglycol (0.58 mL, 10.5 mmol), 90 mL of dry toluene and catalytic amountof pyridinium para-toluene sulfonate. This mixture was refluxed at 140°C. replacing the toluene 3 times and finally allowing the reaction toreflux overnight. The mixture was then distilled to approximately 30 mL,removed from heat and diluted with DCM and extracted with sat. NaHCO₃(×2) then water (×3) to remove any excess ethylene glycol. The productwas purified by column chromatography (DCM:MeOH, 100:0→95:5). Isolatedyield: 0.41 g (65%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.05 (d, J=6.36 Hz, 12H) 1.78 (t,J=7.58 Hz, 15H) 2.16 (t, J=7.58 Hz, 15H) 3.76 (s, 15H) 4.82 (dt,J=12.53, 6.33 Hz, 8 H)¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 21.59 (s,1C) 29.02 (s, 1C) 32.07 (s, 1C) 64.94 (s, 1C) 67.23 (s, 1C) 67.26 (s,1C) 109.84 (s, 1C) 172.56 (s, 1C) C₁₅H₂₆O₆Na¹⁺ low resolution ESI-MScalculated: 302.17, found: 325.0.

3-(2-(3-hydroxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanoic acid (21) and3-(2-(3-isopropoxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanoic acid (22)

Compound (20) (2.1 g, 6.9 mmol) was solvated in 20 mL of MeOH to whichwas added 1.5 eq of LiOH (0.51 g, 21.5 mmol) in 5 mL of water. Thismixture was allowed to stir for 2 h until all starting material wasconsumed. The solution was brought to neutrality by the addition of 1 MHCl. This mixture was purified by column chromatography (DCM:MeOH with1% AcOH, 100:0→90:10). Isolated yield of (21): 0.53 g (35%). Yield of(22): 0.81 g (45%).

(21)

¹H NMR (300 MHz, METHANOL-d₄) δ ppm 1.94 (t, J=8.20 Hz, 4H) 2.33 (t,J=7.30 Hz, 15H) 3.94 (s, 26H)¹³C NMR (75 MHz, METHANOL-d₄) δ ppm 28.19(s, 1C) 31.82 (s, 1C) 64.77 (s, 1C) 109.81 (s, 1C) 175.90 (s, 1C)C₉H₁₄O₆Li⁻ low resolution ESI-MS calculated: 218.07, found: 224.12.

(22)

¹H NMR (500 MHz, METHANOL-d₄) δ ppm 1.22 (d, J=6.36 Hz, 6H) 1.87-2.03(m, 4H) 2.23-2.34 (m, 4H) 3.55 (m, J=5.14 Hz, 3H) 3.67 (m, J=5.14 Hz,3H) 4.89-5.00 (m, 2H)¹³C NMR (126 MHz, METHANOL-d₄) δ ppm 7.75 (s, 1C)20.72 (s, 1C) 28.80 (s, 1C) 31.81 (s, 1C) 60.87 (s, 1C) 62.94 (s, 1C)67.60 (s, 1C) 72.13 (s, 1C) 109.92 (s, 1C) 173.40 (s, 1C) 176.73 (s, 1C)C₁₂H₂₀O₆ ¹⁻ low resolution ESI-MS calculated: 260.12, found: 259.03.

Tributyl(3-(3-(2-(3-isopropoxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanamido)propyl)phosphoniumbromide (24)

Compound (22) (0.3 g, 1.1 mmol) was solvated in 1.5 mL of ACN followedby TBTU (0.39 g, 1.2 mmol), 2.5 eq of triethylamine (0.38 ml) andphosphonium ionic tag (23) (0.45 g, 1.2 mmol). This mixture was allowedto stir for 4 h until the starting material (22) was completelyconsumed. The reaction mixture was diluted with ethyl acetate andextracted with 5% NaHCO₃×2 and once with brine. The organic layer wasdried and concentrated and purified by column chromatography. DCM:MeOH100:0→95:5. Isolated yield: 0.54 g (84%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=6.74 Hz, 9H) 1.06 (d,J=6.45 Hz, 6H) 1.25 (s, 6H) 1.38-1.59 (m, 11H) 1.80-1.95 (m, 7H)2.15-2.30 (m, 9H) 2.18 (t, J=7.03 Hz, 8H) 3.28-3.44 (m, 2H) 3.84 (br.s., 5H) 3.94 (s, 6H) 4.72-4.89 (m, 1H) C₂₇H₅₃NO₆P¹⁺ low resolutionESI-MS calculated: 502.36, found: 502.36.

Tributyl(3-(3-(2-(3-hydroxy-3-oxopropyl)-1,3-dioxolan-2-yl)propanamido)propyl)phosphonium bromide (25)

Compound (24) (0.25 g, 0.4 mmol) was solvated in 2.5 mL of MeOH to whichwas added 10 eq of LiOH (0.1 g, 4 mmol) in mL of water. This mixture wasallowed to stir for 3 h until all starting material was consumed. Thesolution was brought to neutrality by the addition of 1M HCl in MeOH.This mixture was purified by column chromatography (DCM:MeOH with 1%AcOH, 100:0→90:10). Isolated yield of (25): 0.20 g (95%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=6.74 Hz, 9H) 1.25 (s,6H) 1.38-1.59 (m, 11H) 1.96-2.05 (m, 7H) 2.15-2.30 (m, 9H) 2.40 (t,J=7.03 Hz, 8H) 3.28-3.44 (m, 2H) 3.84 (br. s., 5H) 3.94 (s, 6H)C₂₄H₄₇NO₅P¹⁺ low resolution ESI-MS calculated: 460.31, found: 460.30.

5′-DMTr-2′-TIPS-3′-[tributyl(3-(3-(2-(2-carboxyethyl)-1,3-dioxolan-2-yl)propanamido)propyl)phosphoniumbromide] (26)

To a solution of compound (25) (0.2 g, 0.37 mmol) in ACN (1 mL) wasadded TBTU (0.19 g, 0.6 mmol), triethylamine (0.5 mL) and compound (13)(0.42 g, 0.6 mmol). The resulting mixture was allowed to stir for 12 huntil the starting material (25) was completely consumed. The reactionmixture was diluted with ethyl acetate and extracted with 5% NaHCO₃×2and once with brine. The organic layer was dried and concentrated, takenup in minimal amounts of DCM at precipitated in 100 ml of MTBE, filteredover Celite©. Isolated yield of (26): 0.20 g (45%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=6.74 Hz, 9H) 1.02-1.59(m, 38H) 1.96-2.05 (m, 7H) 2.15-2.30 (m, 9H) 2.40 (t, J=7.03 Hz, 8H)3.37-3.40 (m, 4H) 3.78-3.94 (br. m, 17H) 4.15 (d, J=2.77 Hz, 1H)4.63-4.67 (m, 1H) 5.31 (dd, J=5.14, 2.96 Hz, 1H) 5.40-5.46 (m, 1H) 5.42(s, 1H) 5.99 (d, J=6.32 Hz, 1H) 6.87-6.93 (m, 4H) 7.27-7.37 (m, 7H)7.41-7.45 (m, 2H) 7.75 (d, J=8.30 Hz, 1H) C₆₃H₉₅N₃O₁₂PSi¹⁺ lowresolution ESI-MS calculated: 1144.64, found: 1144.7.

2′-TIPS-3′-[(tributyl(3-(7-oxy-4,7-dioxoheptanamido)propyl)phosphoniumchloride] uridine (27)

Compound (26) (0.228 g, 0.199 mmol) was solvated with 15 ml of 80%acetic acid in water and first allowed to stir at room temperature for 6h showing almost no loss of the ketal, but complete loss of the tritylgroup. The reaction was then heated to 50° C. for 12 h which then showedabout a 25% loss of ketal. Then the reaction was placed at 80° C. for 40h which then showed almost complete consumption of starting material.The mixture was diluted with DCM and extracted with 3 portions ofsaturated NaHCO₃. The organic layers were dried with MgSO₄ andconcentrated to dryness. The crude mixture was then solvated in minimalamounts of DCM and precipitated in MTBE to remove trityl and somecleaved TIPS. The compound was then filtered over Celite© and collectedwith DCM. The resulting mixture then had to be purified by columnchromatography (0-15% MeOH in DCM) affording compound 27 in moderateyield of 62%, 0.108 g.

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.90-1.13 (m, 37H) 1.39-1.52 (m,17H) 1.78-1.87 (m, 2H) 1.90-1.95 (m, 1H) 2.00-2.03 (m, 1H) 2.06-2.25 (m,11H) 2.27-2.34 (m, 5H) 2.44-2.60 (m, 4H) 2.73-2.80 (m, 2H) 3.37 (d,J=5.47 Hz, 1H) 3.68-3.92 (m, 3H) 4.16-4.22 (m, 1H) 4.64-4.72 (m, 1H)5.01-5.13 (m, 1H) 5.62-5.72 (m, 1H) 5.78 (dd, J=7.62, 4.49 Hz, 1H) 8.07(d, J=7.82 Hz, 1H) 8.23 (d, J=8.21 Hz, 1H) 8.70-9.11 (m, 1H).

¹³C NMR (101 MHz, CHLOROFORM-d) δ ppm 12.05 (s, 1C) 12.16 (s, 1C) 13.37(s, 1C) 17.66 (s, 1C) 17.67 (s, 1C) 17.75 (s, 1C) 17.77 (s, 1C) 17.79(s, 1C) 17.85 (s, 1C) 18.25 (s, 1C) 18.73 (s, 1C) 21.25 (s, 1C) 23.44(s, 1C) 23.50 (s, 1C) 23.55 (s, 1C) 23.80 (s, 1C) 23.94 (s, 1C) 125.81(s, 1C) 128.58 (s, 1C) 139.39 (s, 1C) 143.40 (s, 1C) 183.06 (s, 1C)207.78 (s, 1C).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 33.29 (s, 1P) 33.36 (s, 1P) 33.42(s, 1P) 33.51 (s, 1P) 33.72 (s, 1P) 33.78 (s, 1P).

C₄0H₇₃N₃O₉PSi⁺¹ low resolution ESI-MS calculated:798.48, found: 798.51.

diisopropyl 4,4-bis(phenylthio)heptanedioate (28)

compound (19) (4.69 g, 18.1 mmol) was solvated in 36.3 mL of DCM (0.5 M)followed by 4.83 mL, 2.6 eq of thiophenol (5.203 g, 47.2 mmol). Thismixture was cooled down to 0° C. in an ice bath then treated, drop-wise,with stirring 5.75 mL of boron trifluoride etherate (BF₃.O(Et)₂) (6.44g, 45.4 mmol). This mixture was stirred and allowed to slowly warm up toroom temperature over night. After 10 hours, the mixture was cooled to0° C. and concentrated NaHCO₃ was added carefully to the solutionquenching the Boron trifluoride followed by DCM to dilute. The mixturewas extracted ×3 with saturated sodium bicarbonate, dried with MgSO₄concentrated to dryness. The compound was purified from excess thiopenolby column chromatography (0-20% Hexanes: ethylacetate) yieldingquantitative conversion.

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 1.21 (d, J=6.64 Hz, 12H) 1.78-2.03(m, 4H) 2.58-2.84 (m, 4H) 4.96 (dt, J=12.60, 6.40 Hz, 2H) 7.30-7.45 (m,6H) 7.62 (d, J=6.64 Hz, 4H).

¹³C NMR (101 MHz, CHLOROFORM-d) δ ppm 21.82 (s, 1C) 30.20 (s, 1C) 32.87(s, 1C) 67.80 (s, 1C) 128.80 (s, 1C) 129.38 (s, 1C) 130.55 (s, 1C)136.83 (s, 1C) 172.42 (s, 1C).

C₂₅H₃₂O₄S₂ low resolution ESI-MS calculated: 460.17, found: 483.23.

4,4-bis(phenylthio)heptanedioic acid (29) and7-isopropoxy-7-oxo-4,4-bis(phenylthio)heptanoic acid (30)

Compound 28 (6.43 g, 14.0 mmol) was solvated in methanol:water 4:1 200ml and cooled to 0° C. in an ice bath. 0.2 eq of NaOH (0.11 g, 2.8 mmol)was solvated in 10 mL of H₂O and added drop-wise to the above solution.This mixture was allowed to react for 12 h then was concentrated toremove a significant amount of methanol, then 1M HCL was added followedby ethyl acetate and extracted ×2 with 1M HCL. The organic layer wasdried with MgSO₄, concentrated to dryness yielding a very complexmixture of compounds. After purifying each spot by column chromatography(0-30% Hexanes: ethylacetate with 1% AcOH) it was determined that notall the methanol was removed and neither was all the HCL, as no brinewash was done at the end and significant transesterification of theisopropyl ester to the methyl ester was observed. The monoester product(30) during this scale-up was completely converted to the methyl esterproduct in 85% yield.

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¹H NMR (400 MHz, DMSO-d₆) δ ppm 1.45-2.01 (m, 4H) 2.50-2.64 (m, 4H)7.35-7.49 (m, 6H) 7.52-7.65 (m, 4H) 12.19 (s, 2H).

¹³C NMR (101 MHz, DMSO-d₆) δ ppm 29.62 (s, 1C) 32.78 (s, 1C) 38.81 (s,1C) 68.19 (s, 1C) 129.54 (s, 1C) 130.05 (s, 1C) 130.44 (s, 1C) 136.77(s, 1C) 174.01 (s, 1C) 178.31 (s, 1C).

C₁₉H₂₀O₄S₂ low resolution ESI-MS calculated: 376.08, found: 399.21.

(30)

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 1.82-2.04 (m, 4H) 2.64-2.84 (m, 4H)3.65 (s, 3H) 7.28-7.45 (m, 6H) 7.54-7.67 (m, 4H).

¹³C NMR (101 MHz, CHLOROFORM-d) δ ppm 29.61 (s, 1C) 29.70 (s, 1C) 32.65(s, 1C) 32.93 (s, 1C) 51.86 (s, 1C) 66.90 (s, 1C) 128.96 (s, 1C) 129.54(s, 1C) 130.30 (s, 1C) 136.75 (s, 1C) 173.46 (s, 1C) 179.34 (s, 1C)183.06 (s, 1C).

C₂₀H₂₂O₄S₂ low resolution ESI-MS calculated: 390.1, found: 413.12.

tributyl(3-(7-methoxy-7-oxo-4,4-bis(phenylthio)heptanamido)propyl)phosphonium bromide (31)

Compound (30) (0.5 g, 1.28 mmol) 1.5 eq of DCC (0.396 g, 1.92 mmol) weresolvated in 5 mL of ACN. Phosphonium tag (23) 1.15 eq (0.62 g, 1.47mmol) was solvated in 2 mL of dry pyridine and added directly to theabove solution followed by catalytic amount of DMAP. The reaction wasallowed to stir for 6 h until the reaction was complete by MS. Thereaction was taken up in ethyl acetate and extracted ×2 with ammoniumchloride and once with brine. The organic layer was dried with magnesiumsulfate and concentrated to dryness. The mixture was purified by columnchromatography to remove excess tag (0-15% MeOH:DCM) and in the processa significant amount of material was lost on the column, yielding 63%,0.54 g.

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.85-1.05 (m, 9H) 1.36-1.63 (m,13H) 1.80-2.04 (m, 7H) 2.17-2.35 (m, 6H) 2.58-2.81 (m, 6H) 3.30-3.46 (m,2H) 3.60 (s, 3H) 7.28-7.40 (m, 6H) 7.59-7.76 (m, 4H) 8.51 (t, J=5.27 Hz,1H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.44 (s, 1C) 13.46 (s, 1C) 16.92(s, 1C) 17.57 (s, 1C) 18.59 (s, 1C) 19.22 (s, 1C) 21.27 (s, 1C) 21.33(s, 1C) 23.63 (s, 1C) 23.69 (s, 1C) 23.88 (s, 1C) 24.08 (s, 1C) 29.66(s, 1C) 30.95 (s, 1C) 31.33 (s, 1C) 32.82 (s, 1C) 33.40 (s, 1C) 39.16(s, 1C) 39.36 (s, 1C) 51.62 (s, 1C) 67.92 (s, 1C) 128.75 (s, 1C) 129.14(s, 1C) 130.82 (s, 1C) 136.91 (s, 1C) 173.24 (s, 1C) 173.57 (s, 1C).

C₃₅H₅₅NO₃PS₂ ⁺ low resolution ESI-MS calculated: 632.92, found: 632.91.

tributyl(3-(6-carboxy-4,4-bis(phenylthio)hexanamido)propyl)phosphoniumchloride (32)

Compound (31) (0.5 g, 0.75 mmol) was solvated in 8 mL of MeOH to whichwas added 5 eq of NaOH (0.15 g, 3.7 mmol) in 2 mL of water. This mixturewas allowed to stir for 3 h until all starting material was consumed.The solution was brought to neutrality by the addition of 1M HCl. Thismixture was purified by HCl extraction followed by brine ×3, dried andconcentrated. Quantitative recovery.

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.98 (t, J=6.59 Hz, 9H) 1.52 (br.s., 13H) 1.88 (d, J=9.67 Hz, 3H) 2.01 (d, J=4.10 Hz, 4H) 2.08-2.25 (m,7H) 2.49-2.64 (m, 4H) 2.68 (t, J=6.59 Hz, 2H) 3.39 (d, J=4.40 Hz, 2H)7.12-7.21 (m, 3H) 7.30-7.41 (m, 6H) 7.65-7.79 (m, 4H) 8.00 (br. s., 1H).

C₃₄H₅₃NO₃PS₂ ⁺ low resolution ESI-MS calculated: 618.32, found: 618.32.

5′-DMTr-2′-TIPS-3′-[(tributyl(3-(7-oxo-4,4-bis(phenylthio)heptanamido)propyl)phosphonium bromide] uridine (34)

Compound (32) (0.56 g, 0.85 mmol) and 2 eq of DCC (0.35 g, 1.7 mmol)were solvated in 8 mL of ACN. To the above solution 2 eq of nucleoside(13) 1.23 g, 1.7 mmol) was added followed by sub stoichiometric amountsof DMAP. The reaction was allowed to stir for 6 h until all startingmaterial was consumed, monitored by MS. The sample was diluted withethyl acetate and extracted with ammonium chloride ×2 and once withbrine. The organic layer was dried with magnesium sulphate andconcentrated to dryness. The mixture was then precipitated inMTBE-Hexanes 50:50 to remove any unreacted DCC then purified by columnchromatography (0-10% MeOH-DCM) affording a mixture of compound (34) and(33) as an inseparable mixture in 89% yield.

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.81-1.15 (m, 31H) 1.35-1.61 (m,13H) 1.75-2.06 (m, 7H) 2.12-2.35 (m, 6H) 2.50-2.94 (m, 6H) 3.26-3.52 (m,4H) 3.77 (s, 6H) 4.19 (d, J=2.34 Hz, 1H) 4.66 (t, J=5.47 Hz, 1H) 5.24(d, J=8.21 Hz, 2H) 5.35 (dd, J=4.88, 2.54 Hz, 1H) 6.09 (d, J=5.86 Hz,1H) 6.03-6.16 (m, 1H) 6.81 (dd, J=8.60, 1.56 Hz, 4H) 7.17-7.36 (m, 17H)7.27-7.28 (m, 1H) 7.59-7.68 (m, 4H) 7.84 (d, J=8.21 Hz, 1H) 8.45 (t,J=5.67 Hz, 1H) 9.36 (br. s., 1H).

¹³C NMR (101 MHz, CHLOROFORM-d) δ ppm 12.03 (s, 1C) 13.44 (s, 1C) 17.60(s, 1C) 17.77 (s, 1C) 18.56 (s, 1C) 19.03 (s, 1C) 23.52 (s, 1C) 23.57(s, 1C) 23.83 (s, 1C) 23.97 (s, 1C) 55.20 (s, 1C) 67.53 (s, 1C) 76.95(s, 1C) 77.26 (s, 1C) 77.48 (s, 1C) 77.59 (s, 1C) 87.45 (s, 1C) 113.25(s, 1C) 113.28 (s, 1C) 127.21 (s, 1C) 128.00 (s, 1C) 128.83 (s, 1C)129.25 (s, 1C) 129.95 (s, 1C) 130.08 (s, 1C) 130.44 (s, 1C) 130.58 (s,1C) 134.71 (s, 1C) 134.93 (s, 1C) 136.74 (s, 1C) 136.82 (s, 1C) 144.05(s, 1C) 150.77 (s, 1C) 158.64 (s, 1C) 158.67 (s, 1C) 163.38 (s, 1C)172.16 (s, 1C) 172.94 (s, 1C).

C₇₃H₁₀₁N₃O₁₀PS₂Si⁺ low resolution ESI-MS calculated: 1302.64, found:1302.45 (DCC failure product: C₄₇H₇₅N₃O₃PS₂+ resolution ESI-MScalculated: 824.50, found: 824.32).

2′-TIPS-3′-[(tributyl(3-(7-oxy-4,7-dioxoheptanamido)propyl)phosphoniumchloride] uridine (27)

Compound (34) (0.51 g, 0.38 mmol) was solvated in 3.8 ml of THF:water8:2 mixture to which 1.5 eq of silver nitrate was added (96 mg, 0.57mmol). A dowdy white ppt was formed. Molecular iodine was then added (48mg, 0.38 mmol). This mixture was allowed to stir for 16 h until allstarting material was consumed. The sample was then filtered fromprecipitated silver iodine over Celite© and washed with ACN. The samplewas then condensed, resuspended in DCM and precipitated in MTBE yieldingpure compound (27) in 91% yield.

See Previous Synthesis of (27) for NMR Data

Compound (37) (0.12 g, 0.105 mmol) was solvated/reacted directly with 10mL of a 3% TFA solution in DCM followed by 2.5 eq of triethylsilane toquench the trityl cation. This reaction was allowed to stir for 10 minbefore 4 mL of methanol was added to further quench the trityl cation.This was followed by 20 mL of toluene then the mixture was concentratedto dryness, taken up in DCM and precipitated in MTBE yielding compound(38) in 95% yield (62 mg, 0.1 mmol).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.78-1.14 (m, 43H) 1.47 (br. s.,18H) 1.66-1.94 (m, 3H) 1.97-2.86 (m, 20H) 2.99-3.23 (m, 1H) 3.34 (br.s., 1H) 3.52-4.01 (m, 3H) 4.16 (br. s., 1H) 4.60-4.80 (m, 1H) 4.93 (br.s., 1H) 5.04-5.24 (m, 1H) 5.72 (br. s., 2H) 7.70 (d, J=7.91 Hz, 1H)7.96-8.28 (m, 2H) 9.20 (br. s., 1H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 12.01 (s, 1C) 12.03 (s, 1C) 12.42(s, 1C) 13.24 (s, 1C) 16.69 (s, 1C) 17.58 (s, 1C) 17.68 (s, 1C) 17.70(s, 1C) 18.06 (s, 1C) 18.14 (s, 1C) 18.69 (s, 1C) 18.78 (s, 1C) 21.32(s, 1C) 23.27 (s, 1C) 23.33 (s, 1C) 23.71 (s, 1C) 23.91 (s, 1C) 26.89(s, 1C) 28.18 (s, 1C) 28.44 (s, 1C) 29.49 (s, 1C) 32.14 (s, 1C) 36.84(s, 1C) 37.34 (s, 1C) 61.24 (s, 1C) 73.45 (s, 1C) 73.66 (s, 1C) 74.04(s, 1C) 83.52 (s, 1C) 88.78 (s, 1C) 89.46 (s, 1C) 92.69 (s, 1C) 102.60(s, 1C) 114.66 (s, 1C) 118.55 (s, 1C) 125.79 (s, 1C) 127.98 (s, 1C)128.61 (s, 1C) 133.49 (s, 1C) 133.90 (s, 1C) 141.68 (s, 1C) 141.79 (s,1C) 150.96 (s, 1C) 163.71 (s, 1C) 163.83 (s, 1C) 170.93 (s, 1C) 171.95(s, 1C) 172.99 (s, 1C) 176.18 (s, 1C) 207.81 (s, 1C).

C₄₀H₇₁N₃O₈PSi+ low resolution ESI-MS calculated: 780.47, found: 780.58.

Compound 41 and 42 Mixture

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.07-0.16 (m, 8H) 0.83-1.05 (m,62H) 1.09-1.28 (m, 9H) 1.33 (d, J=6.15 Hz, 18H) 1.47 (br. s., 20H) 1.91(br. s., 4H) 2.14 (br. s., 11H) 2.21-2.38 (m, 6H) 2.52 (br. s., 2H) 2.64(br. s., 2H) 3.14 (br. s., 1H) 3.21 (s, 1H) 3.27-3.41 (m, 4H) 3.48 (d,J=7.91 Hz, 3H) 3.66 (s, 3H) 3.62 (s, 3H) 3.78 (d, J=5.57 Hz, 12H) 3.89(s, 2H) 4.17-4.35 (m, 4H) 4.50 (br. s., 3H) 4.89 (br. s., 1H) 5.13-5.24(m, 2H) 5.92-6.03 (m, 2H) 6.77-6.87 (m, 6H) 7.13-7.36 (m, 26H) 7.51 (d,J=7.91 Hz, 1H) 7.69-7.74 (m, 2H) 7.80-7.88 (m, 2H).

³¹P NMR (81 MHz, CHLOROFORM-d) 8 ppm −0.91 (s, 1P) −0.36 (s, 1P) 33.91(s, 1P) 33.96 (s, 1P).

C₇₇H₁₁₆N₅O₁₈P₂Si₂+ low resolution ESI-MS calculated: 1516.73, found:1516.62.

tributyl(8-ethoxy-8-oxo-5,5-bis(phenylthio)octyl)phosphonium bromide(42)

Compound (15) (0.82 g, 1.51 mmol) and 3 eq of thiophenol (0.38 mL, 3.0mmol) were solvated with 6 mL of DCM and cooled to 0° C. in an ice bath.Boron trifluoride etherate (0.46 mL, 4.53 mmol) was then added drop-wiseover 10 min. The mixture was allowed to stir at 0° C. for 30 min thenallowed to slowly warm up to room temperature for 4 h. The mixture wasthen cooled to 0° C. again and quenched with saturated sodiumbicarbonate and extracted ×3 with DCM. The organic layers were combined,dried, and concentrated to dryness. The mixture was then purified bychromatography (0-5% DCM-MeOH) affording pure (42) in good yield, 93%.

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.96 (t, J=7.03 Hz, 9H) 1.19-1.28(m, 3H) 1.33-1.60 (m, 17H) 1.73-1.85 (m, 2H) 1.87-1.98 (m, 2H) 2.26-2.38(m, 2H) 2.39-2.52 (m, 7H) 2.63-2.75 (m, 2H) 4.09 (q, J=7.29 Hz, 2H)7.24-7.28 (m, 2H) 7.30-7.42 (m, 5H) 7.63 (dd, J=7.42, 1.95 Hz, 3H).

¹³C NMR (101 MHz, CHLOROFORM-d) δ ppm 13.44 (s, 1C) 14.10 (s, 1C) 18.59(s, 1C) 19.06 (s, 1C) 23.68 (s, 1C) 23.73 (s, 1C) 23.79 (s, 1C) 23.94(s, 1C) 29.77 (s, 1C) 32.86 (s, 1C) 36.85 (s, 1C) 60.46 (s, 1C) 67.75(s, 1C) 128.77 (s, 1C) 129.04 (s, 1C) 129.23 (s, 1C) 130.77 (s, 1C)136.42 (s, 1C) 172.75 (s, 1C).

tributyl(7-carboxy-5,5-bis(phenylthio)heptyl)phosphonium bromide (43)

Compound (42) (0.75 g, 1.2 mmol) was solvated with 5 mL of a 4:1 mixtureof methanol:water and added to that 5 eq of NaOH (0.24 g, 6 mmol) andwas allowed to stir for 2 hours. The reaction was quenched withsaturated sodium bicarbonate, then concentrated to remove the methanol.The mixture was then take up in ethyl acetate and extracted with 1M HClonce and three times with brine. The organic layer was dried withmagnesium sulfate and condensed to dryness producing compound (43) innear quantitative yield.

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.85-1.05 (m, 9H) 1.19-1.42 (m, 4H)1.45 (br. s., 11H) 1.58 (br. s., 2H) 1.75 (br. s., 2H) 1.94 (t, J=7.23Hz, 2H) 2.02 (d, J=1.17 Hz, 1H) 2.11-2.27 (m, 8H) 2.75 (t, J=7.42 Hz,2H) 7.18-7.37 (m, 7H) 7.65 (d, J=7.82 Hz, 4H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.41 (s, 1C) 18.19 (s, 1C) 18.82(s, 1C) 23.44 (s, 1C) 23.50 (s, 1C) 23.74 (s, 1C) 23.93 (s, 1C) 68.37(s, 1C) 76.81 (s, 1C) 77.24 (s, 1C) 77.66 (s, 1C) 128.77 (s, 1C) 129.15(s, 1C) 131.08 (s, 1C) 136.38 (s, 1C) 174.83 (s, 1C).

5′-DMTr-2′-TIPS-3′-[tributyl(7-oxy-5,5-bis(phenylthio)heptyl)phosphonium bromide] uridine (44)

Compound (43) (0.59 g, 0.99 mmol) and 1.5 eq of DCC (0.30 g, 1.48 mmol)were solvated in 9.5 mL of ACN. To the above solution 1.5 eq ofnucleoside (13) (1.03 g, 1.48 mmol) was added followed by substoichiometric amounts of DMAP. The reaction was allowed to stir for 6 huntil all starting material was consumed, monitored by MS. The samplewas diluted with ethyl acetate and extracted with ammonium chloride ×2and once with brine. The organic layer was dried with magnesium sulphateand concentrated to dryness. The mixture was then precipitated inMTBE-Hexanes 50:50 to remove any unreacted DCC then purified by columnchromatography (0-10% MeOH-DCM) affording compound (44) in 83% yield(1.05 g, 0.82 mmol).

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.94-1.18 (m, 39H) 1.32-1.60 (m,23H) 1.64-1.72 (m, 3H) 1.74-1.84 (m, 3H) 1.90-2.17 (m, 15H) 2.76-2.84(m, 2H) 3.42-3.51 (m, 3H) 3.79 (d, J=0.78 Hz, 7H) 4.10-4.15 (m, 2H)4.67-4.71 (m, 1H) 5.26-5.30 (m, 1H) 5.40 (dd, J=5.08, 2.74 Hz, 1H) 6.10(d, J=6.25 Hz, 1H) 6.81-6.85 (m, 5H) 7.21-7.38 (m, 23H) 7.60-7.68 (m,5H) 7.88 (d, J=8.21 Hz, 1H) 8.61 (s, 1H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 12.13 (s, 1C) 13.38 (s, 1C) 17.68(s, 1C) 17.85 (s, 1C) 18.01 (s, 1C) 18.64 (s, 1C) 23.45 (s, 1C) 23.52(s, 1C) 23.76 (s, 1C) 23.96 (s, 1C) 25.02 (s, 1C) 25.65 (s, 1C) 33.86(s, 1C) 55.27 (s, 1C) 67.41 (s, 1C) 76.69 (s, 1C) 77.11 (s, 1C) 77.53(s, 1C) 87.57 (s, 1C) 113.33 (s, 1C) 113.36 (s, 1C) 128.05 (s, 1C)129.00 (s, 1C) 129.43 (s, 1C) 130.02 (s, 1C) 130.15 (s, 1C) 130.71 (s,1C) 130.74 (s, 1C) 134.75 (s, 1C) 134.93 (s, 1C) 136.52 (s, 1C) 144.09(s, 1C) 150.66 (s, 1C) 158.74 (s, 1C) 158.78 (s, 1C) 163.29 (s, 1C)172.20 (s, 1C).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 32.73 (s, 1P).

2′-TIPS-3′-[tributyl(7-oxy-5,5-bis(phenylthio)heptyl) phosphoniumbromide] uridine (45)

Compound (44) (0.76 g, 0.59 mmol) was solvated in 8 ml of THF:water 8:2mixture to which 1.5 eq of silver nitrate was added (150 mg, 0.89 mmol).A dowdy white ppt was formed. Molecular iodine was then added (75 mg,0.59 mmol). This mixture was allowed to stir for 16 h until all startingmaterial was consumed. The sample was then filtered from precipitatedsilver iodine over Celite© and washed with ACN. The sample was thencondensed, resuspended in DCM and precipitated in MTBE yielding purecompound (45) in 70% yield 0.326 g.

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 0.91-1.10 (m, 11H) 1.44-1.57 (m,5H) 1.63 (dd, J=15.90, 8.07 Hz, 1H) 1.78 (dd, J=14.06, 6.97 Hz, 1H)2.29-2.40 (m, 3H) 2.41-2.53 (m, 1H) 2.56-2.85 (m, 3H) 3.76-3.92 (m, 1H)3.98 (s, 1H) 4.11-4.19 (m, 1H) 4.70-4.78 (m, 1H) 5.18 (dd, J=4.89, 3.42Hz, 1H) 5.75 (d, J=8.07 Hz, 1H) 5.81 (d, J=5.62 Hz, 1H) 8.00 (d, J=8.31Hz, 1H) 8.67 (br. s., 1H).

¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 11.93 (s, 1C) 11.96 (s, 1C) 11.98(s, 1C) 13.37 (s, 1C) 17.50 (s, 1C) 17.52 (s, 1C) 17.54 (s, 1C) 17.57(s, 1C) 17.58 (s, 1C) 17.60 (s, 1C) 17.62 (s, 1C) 17.65 (s, 1C) 17.66(s, 1C) 17.67 (s, 1C) 17.69 (s, 1C) 17.71 (s, 1C) 17.72 (s, 1C) 17.78(s, 1C) 17.80 (s, 1C) 18.59 (s, 1C) 18.77 (s, 1C) 18.97 (s, 1C) 19.15(s, 1C) 20.80 (s, 1C) 20.84 (s, 1C) 23.54 (s, 1C) 23.57 (s, 1C) 23.77(s, 1C) 23.88 (s, 1C) 24.35 (s, 1C) 24.47 (s, 1C) 28.00 (s, 1C) 30.88(s, 1C) 36.93 (s, 1C) 41.11 (s, 1C) 61.25 (s, 1C) 73.72 (s, 1C) 73.96(s, 1C) 83.72 (s, 1C) 88.91 (s, 1C) 102.72 (s, 1C) 141.92 (s, 1C) 150.83(s, 1C) 163.77 (s, 1C) 171.98 (s, 1C) 208.11 (s, 1C).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 33.08 (s, 1P).

[5′-DMTr-2′TBDMS-uridine]-[3′-p(OMe)-5]-[2′-TIPS-3′-(tributyl(7-oxy-,5-bis(phenylthio)heptyl) phosphonium bromide)-uridine (46)

Compound (45) (0.326 g, 0.42 mmol) was solvated in 4.2 mL of dry ACN. Tothis mixture was added 1.5 eq of phosphoramidite (39) (0.52 g, 0.63mmol) and 1.6 eq of DCI (82 mg, 0.69 mmol). This mixture was stirred for6 h at room temperature at which point an MS showed complete consumptionof starting material. 0.5 mL of tert-butanol was then added to themixture to react with excess phosphoramidite and make it more soluble inthe MTBE mixture. The mixture was then precipitated into MTBE:hexanes50:50 to remove the excess amidite and butanol. The solid precipitatewas solvated in DCM and treated with 0.5 mL of tert-bury hydroperoxidein decane (5M) to oxidize the internucleotide phosphate. The mixture wasthen precipitated into MTBE to remove the excess peroxide, decane, DCI,and residual amidite that might remain. This afforded pure (46) in 96%yield.

¹H NMR (300 MHz, CHLOROFORM-d) 8 ppm −0.05-0.20 (m, 7H) 0.86 (s, 15H)0.89-1.02 (m, 35H) 1.10-1.29 (m, 8H) 1.35 (d, J=6.15 Hz, 16H) 1.48 (br.s., 16H) 1.74 (br. s., 2H) 2.19 (br. s., 10H) 2.60 (d, J=14.07 Hz, 4H)2.66-2.77 (m, 1H) 3.20 (s, 1H) 3.27-3.41 (m, 3H) 3.46 (br. s., 2H)3.52-3.71 (m, 2H) 3.71-3.80 (m, 7H) 3.89 (s, 1H) 4.05 (br. s., 1H) 4.13(br. s., 1H) 4.43-4.56 (m, 2H) 5.06-5.22 (m, 2H) 5.60-5.77 (m, 1H)5.82-6.05 (m, 2H) 6.76-6.87 (m, 5H) 7.17-7.38 (m, 16H) 7.41-7.58 (m, 2H)7.72-7.98 (m, 2H).

³¹P NMR (81 MHz, CHLOROFORM-d) 8 ppm −1.07 (s, 1P) −0.30 (s, 1P) 33.31(s, 1P) 33.35 (s, 1P).

C₇₅H₁₁₅N₄O₁₈P₂Si₂+ low resolution ESI-MS calculated: 1477.72, found:1477.62.

Isopropyl 3-(2-(3-hydroxypropyl)-1,3-dioxolan-2-yl)propanoate, (II)

Compound (67) (0.334 g, 1.35 mmol) was dissolved in 13.5 mL making a0.1M solution. This mixture was cooled to 0° C. and borane, and 1M inTHF (1.75 mL. 1.75 mmol) was added drop wise. Once the vigorous releaseof hydrogen subsided, the ice bath was removed and the reaction wasallowed to stir for 2 hours until the reaction was complete as shown byTLC. The mixture was quenched by first cooling the solution back down to0° C. and adding methanol slowly until the release of hydrogen subsided.The crude reaction mixture was then concentrated to dryness, taken up inmethanol once more and concentrated again to ensure removal of trimethylborate. The mixture was purified by column chromatography 100% hexanesto 50:50 hexanes:ethyl acetate yielding pure primary hydroxyl 95%, 0.315g.

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.11 (d, J=6.11 Hz, 6H) 1.46-1.68(m, 6H) 1.82-1.94 (m, 3H) 2.17-2.32 (m, 3H) 3.43-3.61 (m, 2H) 3.84 (s,4H) 4.88 (dt, J=12.53, 6.33 Hz, 1H).

¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 21.67 (s, 1C) 26.85 (s, 1C) 29.14(s, 1C) 29.69 (s, 1C) 31.90 (s, 1C) 33.68 (s, 1C) 62.46 (s, 1C) 64.91(s, 1C) 67.52 (s, 1C) 110.69 (s, 1C) 173.07 (s, 1C).

Isopropyl 3-(2-(3-bromopropyl)-1, 3-dioxolan-2-yl)propanoate (III)

Compound (II) (0.32 g, 1.58 mmol) was dissolved in 10 mL of DCM and 2 mLof triethylamine and cooled to 0° in an ice bath. To this solution PBr₃(0.225 mL, 2.37 mmol) was added drop wise over 10 min and allowed tostir for 1 h at zero degrees until the reaction was complete by TLC. Thereaction was quenched with saturated sodium bicarbonate diluted withethyl acetate and extracted with brine twice. The organic layer wasdried, concentrated and purified by a short silica plug with a 70:30Hexanes:ethyl acetate yielding 0.45 g, 1.455 mmol of compound (III).

¹H NMR (500 MHz, CHLOROFORM-d) d=5.01-4.87 (m, 1H), 3.97-3.82 (m, 4H),3.36 (t, J=6.7 Hz, 2H), 2.33-2.20 (m, 2H), 1.96-1.82 (m, 4H), 1.73-1.64(m, 2H), 1.16 (d, J=6.4 Hz, 6H).

¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 21.75 (s, 1C) 27.20 (s, 1C) 29.12(s, 1C) 32.11 (s, 1C) 33.85 (s, 1C) 35.69 (s, 1C) 64.95-65.08 (s, 1C)67.47 (s, 1C) 110.26 (s, 1C) 172.81 (s, 1C).

Tributyl(3-(2-(3-isopropoxy-3-oxopropyl)-1,3-dioxolan-2-yl)propyl)phosphoniumbromide (IV)

Compound (III) (0.33 g, 1.06 mmol) was dissolved with 4 mL of ACN. Tothis mixture tributylphosphine (0.53 ml, 2.12 mmol) was added directlyand heated to 80° C. This was allowed to stir for 6 h. The mixture wasconcentrated and diluted with acetone then triturated into 250 mL ofhexanes. The precipitate was filtered and the hexanes discarded. Thisprocess was repeated once more and the resulting goo was pure ionicallytagged compound (IV) in near quantitative yield, 0.54 g, 1.05 mmol.

¹H NMR (CHLOROFORM-d, 200 MHz): δ=4.91 (quin, J=6.3 Hz, 1H), 3.97-3.82(s, 4H), 2.56-2.72 (m, 2H), 2.23-2.55 (m, 10H), 1.66-1.99 (m, 6H),1.35-1.61 (m, 16H), 1.08-1.26 (m, 7H), 0.80-1.02 ppm (m, 12H).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 32.96 (s, 82P).

Tributyl(7-isopropoxy-7-oxo-4,4-bis(phenylthio)heptyl)phosphoniumbromide (V)

Compound (IV) (0.156 g, 0.30 mmol) was dissolved in 8 mL of dry DCM with5 eq of thiophenol (0.193 mL, 1.52 mmol) followed by 5 eq of borontrifluoride etherate (0.157 mL, 1.52 mmol) and approximately 1 gram ofcrushed 3 Å molecular sieves. This mixture was stirred for 12 h at whichpoint the reaction was filtered over Celite® to remove the sieves. Inthe collection flask was 40 mL of saturated sodium bicarbonate. Thebiphasic mixture was transferred to a separatory funnel and extractedthree times with bicarbonate and once with brine. The organic layer wasdried and concentrated; the resulting oil was purified by precipitationin hexanes/MTBE 75:25, resulting in pure compound (V) in 81% recoveredyield, 0.162 g, 0.24 mmol.

¹H NMR (200 MHz, CHLOROFORM-d) δ ppm 0.80-1.02 (m, 12H) 1.08-1.26 (m,7H) 1.35-1.61 (m, 16H) 1.66-1.99 (m, 6H) 2.23-2.55 (m, 10H) 2.56-2.72(m, 2H) 4.91 (quin, J=6.25 Hz, 1H) 7.30-7.43 (m, 5H) 7.52-7.62 (m, 4H).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 33.29 (s, 1P).

Tributyl(6-carboxy-4,4-bis(phenylthio)hexyl)phosphonium bromide(VI)

Compound (V) (0.75 g, 1.19 mmol) was first dissolved in 3 mL of THF andthen was treated with 30 mL of 0.2 M solution of KOH in water:THF 50:50.This mixture was allowed to stir vigorously for 1 hour, until thehydrolysis was complete by TLC. The mixture was acidified by theaddition of 20 mL of 1M HCl and excess NaCl was added as well. Theorganic layer was diluted with ethyl acetate and extracted three timeswith brine, dried and concentrated to dryness. This afforded pure taggedacid, (VI) in quantitative yield.

¹H NMR 400 MHz, CHLOROFORM-d) δ ppm 0.82-1.02 (m, 9H) 1.28-1.51 (m, 12H)1.58 (br. s., 2H) 1.75 (br. s., 2H) 1.94 (t, J=7.23 Hz, 2H) 2.10-2.32(m, 8H) 2.75 (t, J=7.42 Hz, 2H) 7.27-7.37 (m, 6H) 7.65 (d, J=7.82 Hz,4H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.41 (s, 1C) 18.19 (s, 1C) 18.82(s, 1C) 21.44 (s, 1C) 23.44 (s, 1C) 23.50 (s, 1C) 23.74 (s, 1C) 23.93(s, 1C) 30.10 (s, 1C) 32.76 (s, 1C) 36.32 (s, 1C) 68.37 (s, 1C) 128.76(s, 1C) 129.14 (s, 1C) 131.08 (s, 1C) 136.38 (s, 1C) 174.83 (s, 1C).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 32.89 (s, 1P).

5′-DMTr-2′-TIPS-3′-[tributyl(7-oxy-4,4-bis(phenylthio)hexyl) phosphoniumbromide] uridine (VII)

Compound (VI) (0.294 g, 0.49 mmol) and 1.5 equivalents of DCC (0.14 g,0.76 mmol) were dissolved in 9.5 mL of ACN. To the above solution 1.5 eqof nucleoside (13) (0.54 g, 0.76 mmol) was added followed by substoichiometric amounts of DMAP. The reaction was allowed to stir for 6 huntil all starting material was consumed, monitored by MS. The samplewas diluted with ethyl acetate and extracted with ammonium chloride ×2and once with brine. The organic layer was dried with magnesium sulphateand concentrated to dryness. The mixture was then precipitated inMTBE-Hexanes 50:50 to remove any unreacted DCC then purified by columnchromatography (0.2 mL 10% MeOH-DCM) affording compound(VII) in 82%yield (0.48 g, 0.40 mmol).

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.94-1.18 (m, 39H) 1.32-1.60 (m,21H) 1.64-1.72 (m, 3H) 1.74-1.84 (m, 3H) 1.90-2.17 (m, 15H) 2.76-2.84(m, 2H) 3.42-3.51 (m, 3H) 3.79 (d, J=0.78 Hz, 7H) 4.10-4.15 (m, 2H)4.67-4.71 (m, 1H) 5.26-5.30 (m, 1H) 5.40 (dd, J=5.08, 2.74 Hz, 1H) 6.10(d, J=6.25 Hz, 1H) 6.81-6.85 (m, 5H) 7.21-7.38 (m, 23H) 7.60-7.68 (m,5H) 7.88 (d, J=8.21 Hz, 1H) 8.61 (s, 1H).

¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 12.13 (s, 1C) 13.38 (s, 1C) 17.68(s, 1C) 17.85 (s, 1C) 18.01 (s, 1C) 18.64 (s, 1C) 23.45 (s, 1C) 23.52(s, 1C) 23.76 (s, 1C) 23.96 (s, 1C) 25.02 (s, 1C) 25.65 (s, 1C) 33.86(s, 1C) 55.27 (s, 1C) 67.41 (s, 1C) 76.69 (s, 1C) 77.11 (s, 1C) 77.53(s, 1C) 87.57 (s, 1C) 113.33 (s, 1C) 113.36 (s, 1C) 128.05 (s, 1C)129.00 (s, 1C) 129.43 (s, 1C) 130.02 (s, 1C) 130.15 (s, 1C) 130.71 (s,1C) 130.74 (s, 1C) 134.75 (s, 1C) 134.93 (s, 1C) 136.52 (s, 1C) 144.09(s, 1C) 150.66 (s, 1C) 158.74 (s, 1C) 158.78 (s, 1C) 163.29 (s, 1C)172.20 (s, 1C).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 32.73 (s, 1P).

Low resolution MS, m/z calc: 1231.6 found: 1231.5.

2′-TIPS-3′-[tributyl(6-oxy-4-oxohexyl)phosphonium bromide] uridine(VIII)

Compound (VII) (1.44 g, 1.1 mmol) was dissolved in 10 ml of MeOH:water8:2 mixture to which 20 mol % of molecular iodine (0.06 g, 0.22 mmol)was added. This was shortly followed by 4 equivalents of 30% hydrogenperoxide (0.5 mL, 4.4 mmol). This mixture was allowed to stir for 2 huntil all starting material was consumed. This mixture was first dilutedwith ethyl acetate then quenched by extracting with 10% solution ofsodium thiosulfite, then brine three times. Although the compound couldbe purified by precipitation alone, a column was run to ensure thehighest purity. This provided the deprotected monomer (VIII) in goodyield of 85%. This reaction does yield higher results if no columnchromatography is used. 1.03 g.

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 0.91-1.10 (m, 11H) 1.44-1.57 (m,5H) 1.63 (dd, J=15.90, 8.07 Hz, 1H) 1.78 (dd, J=14.06, 6.97 Hz, 1H)2.29-2.40 (m, 3H) 2.41-2.53 (m, 1H) 2.56-2.85 (m, 3H) 3.76-3.92 (m, 1H)3.98 (s, 1H) 4.11-4.19 (m, 1H) 4.70-4.78 (m, 1H) 5.18 (dd, J=4.89, 3.42Hz, 1H) 5.75 (d, J=8.07 Hz, 1H) 5.81 (d, J=5.62 Hz, 1H) 8.00 (d, J=8.31Hz, 1H) 8.67 (br. s., 1H).

¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 11.93 (s, 1C) 11.96 (s, 1C) 11.98(s, 1C) 13.37 (s, 1C) 17.50 (s, 1C) 17.52 (s, 1C) 17.54 (s, 1C) 17.57(s, 1C) 17.58 (s, 1C) 17.60 (s, 1C) 17.62 (s, 1C) 17.65 (s, 1C) 17.66(s, 1C) 17.67 (s, 1C) 17.69 (s, 1C) 17.71 (s, 1C) 17.72 (s, 1C) 17.78(s, 1C) 17.80 (s, 1C) 18.59 (s, 1C) 18.77 (s, 1C) 18.97 (s, 1C) 19.15(s, 1C) 20.80 (s, 1C) 20.84 (s, 1C) 23.54 (s, 1C) 23.57 (s, 1C) 23.77(s, 1C) 23.88 (s, 1C) 24.35 (s, 1C) 24.47 (s, 1C) 28.00 (s, 1C) 30.88(s, 1C) 36.93 (s, 1C) 41.11 (s, 1C) 61.25 (s, 1C) 73.72 (s, 1C) 73.96(s, 1C) 83.72 (s, 1C) 88.91 (s, 1C) 102.72 (s, 1C) 141.92 (s, 1C) 150.83(s, 1C) 163.77 (s, 1C) 171.98 (s, 1C) 208.11 (s, 1C).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 33.08 (s, 1P).

Low resolution MS, m/z calc: 1029.6 found: 1029.5.

Compound (46) (0.12 g, 0.08 mmol) was solvated in minimal amounts ofACN, approximately 1 ml, then treated with 10 eq of a 0.5 M hydrazinehydrate solution in pyridine:acetic acid (3:2) (40 mg, 0.8 mmol) andallowed to stir for 15 min. The reaction progress was monitored by MS toconfirm consumption of starting material. At this point 10 eq of2,4-pentanedione was added to the solution to quench any excesshydrazine (80 mg, 0.8 mmol. The reaction was then diluted with ethylacetate and extracted with first a saturated ammonium chloride solutionthen ×2 with a 5% solution ammonium chloride solution, then once withbrine. The organic layer was dried and concentrated. The mixture wasthen taken up in minimal amounts of DCM and precipitated in a 75/25mixture of MTBE/hexanes mixture. The oily precipitate was filtered offand the ether layer was concentrated to dryness. The crude concentratewas then purified by column chromatography (0→75% ethyl acetate:hexanes)yielding isomerically pure (47) in 84% yield, 76 mg.

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.09-0.15 (m, 6H) 0.87-1.20 (m,40H) 1.94-2.00 (m, 1H) 2.10-2.20 (m, 2H) 3.44 (br. s., 3H) 3.67-3.79 (m,12H) 4.04-4.23 (m, 5H) 4.28-4.35 (m, 2H) 4.38-4.48 (m, 2H) 4.81-4.90 (m,1H) 5.38 (d, J=8.21 Hz, 1H) 5.64 (d, J=8.20 Hz, 1H) 5.81-5.91 (m, 2H)6.90 (d, J=7.91 Hz, 5H) 7.24-7.37 (m, 9H) 7.41-7.52 (m, 4H) 7.71 (dd,J=8.20, 2.64 Hz, 1H) 9.62 (br. s., 1H).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 0.58 (s, 1P) 0.83 (s, 1P).

3-Nitro-4-ethyl-benzoic acid (49_A)

Fuming nitric acid (90%) (150 ml) was cooled with stirring to −10° C.and 4-ethyl benzoic acid (49) (30 g, 0.2 moles; Sigma-Aldrich) was addedslowly over 30 min directly into the sitting solution (1.33 mmol/ml of(49) to fuming nitric acid). The mixture was then allowed to stir for 30min after addition was complete. The mixture was then poured overapproximately 600 g of crushed ice to quench the reaction. The productformed a white ppt which can be filtered over a sintered glass funnel.The excess ice melted by washing the product with water. The sample wasthen re-crystallized from ethyl acetate/hexanes. Two rounds ofcrystallization were preformed. Yield: 37.2 g (95%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.33 (t, J=7.58 Hz, 3H) 2.99 (q,J=7.58 Hz, 2H) 7.52 (d, J=8.07 Hz, 1H) 8.23 (dd, J=8.07, 1.71 Hz, 1H)8.58 (d, J=1.71 Hz, 1H)¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 14.62 (s,1C) 26.38 (s, 1C) 126.37 (s, 1C) 128.29 (s, 1C) 131.67 (s, 1C) 133.87(s, 1C) 144.85 (s, 1C) 149.36 (s, 1C) 170.40 (s, 1C) C₉H₉NO₄Na¹⁺ lowresolution ESI-MS calculated: 195.05, found: 218.2.

tert-Butyl 3-nitro-4-ethyl-benzoate (50)

Compound (49_A) (19.65 g 0.10 moles) was solvated in 500 ml of THF (0.2M) followed by 1.15 eq (10.14 g, 0.15 moles) of diisopropylcarbodimide.This mixture was allowed to stir for 5 min followed by 1.5 eq oftert-butanol (17.9 mL) and catalytic amounts of4-(dimethylamino)-pyridine. The mixture was allowed to stir for 60 hbefore the reaction was complete. The reaction was diluted with diethylether and filtered to remove the diisopropylurea (DIU) and condensed todryness. The mixture was solvated in ethyl acetate and extracted with 5%NaHCO₃. The product was separated from (74) by column chromatography(solvent system: hexanes:DCM 100:0→0:100). Yield of (50): 15.1 g (60%).

(50)

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 1.26 (t, J=7.47 Hz, 3H) 1.57 (s,11H) 2.91 (q, J=7.33 Hz, 2H) 7.40 (d, J=7.91 Hz, 1H) 8.08 (dd, J=7.91,1.47 Hz, 1H) 8.38 (d, J=1.47 Hz, 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm14.70 (s, 1C) 26.18 (s, 1C) 28.05 (s, 1C) 76.64 (s, 1C) 77.06 (s, 1C)77.49 (s, 1C) 82.13 (s, 1C) 125.42 (s, 1C) 131.12 (s, 1C) 131.18 (s, 1C)133.23 (s, 1C) 143.00 (s, 1C) 149.12 (s, 1C) 163.56 (s, 1C)C₁₃H₁₇NO₄Na¹⁺ low resolution ESI-MS calculated: 251.11, found: 274.32.

(DCC Failure Product)

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.94 (d, J=6.45 Hz, 6H) 1.26 (t,J=7.47 Hz, 3H) 1.39 (d, J=6.74 Hz, 6H) 2.91 (q, J=7.33 Hz, 2H) 3.80 (dq,J=13.88, 6.70 Hz, 1H) 4.44 (quin, J=6.74 Hz, 1H) 6.49 (d, J=7.91 Hz, 1H)7.40 (d, J=8.20 Hz, 1H) 7.67 (dd, J=7.91, 1.76 Hz, 1H) 8.02 (d, J=1.76Hz, 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 14.80 (s, 1C) 20.75 (s, 1C)22.04 (s, 1C) 26.12 (s, 1C) 42.96 (s, 1C) 49.54 (s, 1C) 76.63 (s, 1C)77.05 (s, 1C) 77.48 (s, 1C) 123.13 (s, 1C) 130.76 (s, 1C) 131.52 (s, 1C)135.78 (s, 1C) 141.49 (s, 1C) 148.95 (s, 1C) 153.60 (s, 1C) 168.67 (s,1C) C₁₆H₂₃N₃O₄Na¹⁺ low resolution ESI-MS calculated: 321.16, found:344.23.

tert-Butyl 4-(1-hydroxypropan-2-yl)-3-nitrobenzoate (51)

Compound (750) (10.5 g, 41.7 mmol) was solvated in 19 mL of DMF (2.2M)to which 1.5 eq (1.88 g) of paraformaldehyde was added followed by asolution of potassium tert-butoxide (0.12 eq, 0.56 g) in tert-butanol(5.7 mL). This mixture was allowed to stir at room temperature for 10min before being brought up 90° C. for 3 h. The mixture was thenacidified to neutrality by the addition of a 1M HCl monitored a by a pHmeter. This mixture was then diluted with sat. NaCl and ethyl acetate(×2). Compound (51) was purified by column chromatography in DCM:ethylacetate 100:0→90:10. Yield: 9.4 g (85%).

¹H NMR (400 MHz, ACETONITRILE-d₃) δ ppm 1.41 (d, J=7.03 Hz, 3H) 3.80(sxt, J=6.88 Hz, 1H) 4.49-4.67 (m, 2H) 7.40 (d, J=7.91 Hz, 1H) 8.08 (dd,J=7.91, 1.47 Hz, 1H) 8.38 (d, J=1.47 Hz, 1H)¹³C NMR (75 MHz,CHLOROFORM-d) δ ppm 17.35 (s, 1C) 27.96 (s, 1C) 36.57 (s, 1C) 67.01 (s,1C) 82.27 (s, 1C) 124.77 (s, 1C) 128.50 (s, 1C) 131.04 (s, 1C) 131.06(s, 1C) 132.81 (s, 1C) 142.62 (s, 1C) 150.41 (s, 1C) 163.58 (s, 1C)C₁₄H₁₉NO₅Na¹⁺ low resolution ESI-MS calculated: 281.12, found: 304.02.

tert-Butyl 4-(1-(F-moc)propan-2-yl)-3-nitrobenzoate (52)

Compound (51) (5.38 g, 20.2 mmol) was co-evaporated with pyridine (×3)and solvated in 97 mL of ACN (0.2M) and 2 eq of pyridine (3.13 mL, 38.7mmol). Fmoc-Cl (5.0 g, 19.33 mmol) was added directly to solution andwas allowed to stir for 16 h in the dark, covered with aluminum foil.The reaction went to completion by TLC. The solution was extracted (×3)with 5% ammonium chloride and once with brine and purified by columnchromatography Hex/EtAc 100:0-75:25. Isolated yield: 8.19 g (86%).

¹H NMR (500 MHz, ACETONITRILE-d₃) δ ppm 1.30 (d, J=7.09 Hz, 3H) 1.60 (s,9H) 3.65 (sxt, J=6.94 Hz, 1H) 4.19 (t, J=6.24 Hz, 1H) 4.23-4.34 (m, 2H)4.39-4.53 (m, 2H) 7.27-7.34 (m, 2H) 7.41 (t, J=7.46 Hz, 2H) 7.53 (d,J=7.34 Hz, 2H) 7.62 (d, J=8.31 Hz, 1H) 7.80 (d, J=7.58 Hz, 2H) 8.13 (dd,J=8.19, 1.59 Hz, 1H) 8.28 (d, J=1.71 Hz, 1H)¹³C NMR (126 MHz,ACETONITRILE-d₃) δ ppm −0.10 (s, 1C) 0.06 (s, 1C) 0.23 (s, 1C) 0.40 (s,1C) 0.56 (s, 1C) 0.73 (s, 1C) 0.89 (s, 1C) 16.83 (s, 1C) 27.30 (s, 1C)27.32 (s, 1C) 33.47 (s, 1C) 46.64 (s, 1C) 68.89 (s, 1C) 70.90 (s, 1C)82.13 (s, 1C) 117.34 (s, 1C) 120.06 (s, 1C) 124.56 (s, 1C) 124.87 (s,1C) 124.90 (s, 1C) 127.17 (s, 1C) 127.18 (s, 1C) 127.81 (s, 1C) 127.83(s, 1C) 128.87 (s, 1C) 131.72 (s, 1C) 132.75 (s, 1C) 141.03 (s, 1C)141.17 (s, 1C) 143.50 (s, 1C) 143.55 (s, 1C) 150.42 (s, 1C) 154.54 (s,1C) 163.26 (s, 1C) C₂₉H₂₉NO₇Na¹⁺ low resolution ESI-MS calculated:503.19, found: 526.41.

4-(1-(Fmoc)propan-2-yl)-3-nitrobenzoic acid (52_A)

Compound (52) (8.9 g, 17.7 mmol) was directly solvated in a solution of80% TFA in DCM (50 mL) and allowed to stir for 30 min, until allstarting material had been consumed. The sample was then evaporated todryness on the rotovap and purified by column chromatography, Hex/EtAc100:0-60:40. Isolated yield: 6.09 g (77%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 1.43 (d, J=6.85 Hz, 3H) 3.86 (sxt,J=6.80 Hz, 1H) 4.32-4.46 (m, 4H) 7.28-7.36 (m, 2H) 7.41 (t, J=7.58 Hz,2H) 7.57 (dd, J=6.97, 4.52 Hz, 2H) 7.65 (d, J=8.07 Hz, 1H) 7.76 (d,J=7.34 Hz, 2H) 8.29 (dd, J=8.07, 1.71 Hz, 1H) 8.53 (d, J=1.71 Hz, 1H)11.69 (br. s., 1H)¹³C NMR (126 MHz, CHLOROFORM-d) δ ppm 17.58 (s, 1C)33.71 (s, 1C) 46.62 (s, 1C) 70.08 (s, 1C) 71.14 (s, 1C) 76.80 (s, 1C)77.05 (s, 1C) 77.31 (s, 1C) 120.06 (s, 1C) 125.10 (s, 1C) 125.11 (s, 1C)126.16 (s, 1C) 127.16 (s, 1C) 127.17 (s, 1C) 127.91 (s, 1C) 127.93 (s,1C) 128.87 (s, 1C) 129.00 (s, 1C) 133.71 (s, 1C) 141.26 (s, 1C) 141.27(s, 1C) 142.82 (s, 1C) 143.14 (s, 1C) 143.20 (s, 1C) 150.39 (s, 1C)155.00 (s, 1C) 169.79 (s, 1C) C₂₅H₂₀NO₇ ¹⁻ low resolution ESI-MScalculated: 447.13, found: 446.0.

Phosphonium Tag 4-(1-(Fmoc)propan-2-yl)-3-nitrobenzoate (54)

Compound (52_A) (3.726 g, 8.33 mmol) was solvated in half the solvent(ACN:Py, 28 mL:1.25 mL) to which was added a solution of the phosphoniumtag (53) (3.86 g, 9.16 mmol) in the other half of the solvent, followeddirectly by TBTU (4.0 g, 12.5 mmol). The solution was allowed to stirovernight and by morning the reaction was complete (12 h), and wasconcentrated to half solvent volume then extracted with ethyl acetateand 5% NaHCO₃ (×3) and once with brine. The organic layer was dried withMgSO₄ and condensed to dryness. The compound was then precipitated in500 mL of MTBE to remove the excess pyridine and TBTU byproduct. Theprecipitated white goo was filtered and collected over Celite© thenpurified by column chromatography, DCM:MeOH 100:0→92:8. Isolated yieldof (54): 5.52 g (86%).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.81-0.99 (m, 8H) 1.35 (d, J=7.03Hz, 3H) 1.38-1.61 (m, 11H) 1.99-2.38 (m, 8H) 2.66 (br. s., 2H) 3.54-3.83(m, 3H) 4.10-4.41 (m, 5H) 7.21-7.44 (m, 4H) 7.57 (dd, J=10.11, 8.06 Hz,3H) 7.72 (d, J=7.33 Hz, 2H) 8.55 (d, J=1.76 Hz, 1H) 8.70 (dd, J=8.20,1.76 Hz, 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.35 (s, 1C) 17.68 (s,1C) 18.59 (s, 1C) 19.22 (s, 1C) 23.55 (s, 1C) 23.62 (s, 1C) 23.81 (s,1C) 24.01 (s, 1C) 33.40 (s, 1C) 46.62 (s, 1C) 69.91 (s, 1C) 71.36 (s,1C) 76.67 (s, 1C) 77.09 (s, 1C) 77.52 (s, 1C) 119.96 (s, 1C) 124.31 (s,1C) 125.21 (s, 1C) 127.18 (s, 1C) 127.83 (s, 1C) 128.61 (s, 1C) 131.93(s, 1C) 133.41 (s, 1C) 139.59 (s, 1C) 141.19 (s, 1C) 143.27 (s, 1C)143.33 (s, 1C) 150.18 (s, 1C) 154.87 (s, 1C) 165.19 (s, 1C) ³¹P NMR (81MHz, CHLOROFORM-d) δ ppm 35.07 (s, 1P) C₄₀H₅₃NO₇P¹⁺ low resolutionESI-MS calculated: 690.30, found: 690.35.

Phosphonium Tag 4-(1-hydroxypropan-2-yl)-3-nitrobenzoate (55)

To compound (54) (6.408 g, 9.29 mmol) was added a 20% solution of4-methylpiperidine in DMF (20 ml). After 2 h the reaction was completeby TLC and the solution was evaporated to dryness, then taken up in DCMand precipitated in 500 ml of MTBE to yield 3.09 g of (55) (71%).

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.91 (t, J=7.03 Hz, 11H) 1.26 (d,J=7.03 Hz, 3H) 1.38-1.59 (m, 13H) 1.98 (d, J=7.03 Hz, 2H) 2.11-2.28 (m,7H) 2.36-2.51 (m, 2H) 3.40-3.59 (m, 3H) 3.64-3.82 (m, 2H) 7.51 (d,J=8.21 Hz, 1H) 8.22 (d, J=8.21 Hz, 1H) 8.26 (s, 1H) C₂₅H₄₃NO₅P¹⁺ lowresolution ESI-MS calculated: 468.28, found: 468.28.

Tributyl(3-(4-ethyl-3-nitrobenzamido)propyl)phosphonium bromide (56)

To a solution of 3-nitro-4-ethyl-benzoic acid (49) (3.15 g, 16.1 mmol)and diisopropylethylamine (4 eq, 11.25 ml) in ACN (30 mL) was addedcompound (23) (1.3 eq, 20.9 mmol) and TBTU (1.3 eq, 6.74 g, 20.9 mmol).This mixture was allowed to stir for 12 h. The dark brown solution wasconcentrated to a viscous oil, and taken up in DCM and precipitated in500 ml of MTBE. The solid was collected and re-purified by silica gelcolumn chromatography (DCM:MeOH, 100:0→85:15) eluting as very darkyellow oil. Isolated yield: 7.07 g (84%).

¹H NMR (500 MHz, CHLOROFORM-d) δ ppm 0.90 (t, J=6.97 Hz, 9H) 1.24 (t,J=7.46 Hz, 3H) 1.35-1.56 (m, 12H) 1.96 (d, J=8.07 Hz, 2H) 2.05-2.19 (m,7H) 2.25-2.38 (m, 2H) 2.78 (s, 2H) 2.87 (q, J=7.34 Hz, 2H) 3.60 (q,J=5.79 Hz, 2H) 7.40 (d, J=8.07 Hz, 1H) 7.78 (t, J=5.50 Hz, 1H) 8.07 (d,J=8.07 Hz, 1H) 8.37 (s, 1H) NMR (126 MHz, CHLOROFORM-d) δ ppm 13.21 (s,1C) 14.61 (s, 1C) 18.17 (s, 1C) 18.56 (s, 1C) 23.33 (s, 1C) 23.37 (s,1C) 23.76 (s, 1C) 23.88 (s, 1C) 25.97 (s, 1C) 38.57 (s, 1C) 76.77 (s,1C) 77.02 (s, 1C) 77.28 (s, 1C) 123.82 (s, 1C) 131.09 (s, 1C) 131.47 (s,1C) 132.89 (s, 1C) 141.77 (s, 1C) 149.21 (s, 1C) 165.48 (s, 1C)C₂₄H₄₂N₂O₃P¹⁺ low resolution ESI-MS calculated: 437.29, found: 437.30.

Tributyl(3-(4-(1-hydroxypropan-2-yl)-3-nitrobenzamido)propyl)phosphonium bromide (57)

To a solution of compound (56) (3.56 g, 6.89 mmol) dry DMSO (13.8 mL),was added para-formaldehyde (2.1 eq, 0.43 g, 14.4 mmol). This mixturewas sonicated for 20 min until all of para-formaldehyde dissolved. Theresulting mixture was treated with 1.5 eq of potassium tert-butoxide(1.16 g, 10.3 mmol). The reaction turned a dark purple immediately. Thereaction was allowed to stir for 12 h at room temperature. The reactionwas monitored by MS, showing the disappearance of the starting material.The reaction was treated with 1M HCl in MeOH to bring to neutrality atwhich point the reaction was precipitated in diethyl ether, and then inDCM. This last precipitation step separated the product from unreactedpara-formaldehyde. The product was purified by reverse phasechromatography, using 100 mM TEAA buffer in water (pH 7): ACN80:20-20:80. Isolated yield: 1.3 g (35%).

¹H NMR (400 MHz, CHLOROFORM-d) δ ppm 0.84-0.98 (m, 9H) 1.26 (d, J=7.03Hz, 3H) 1.38-1.59 (m, 11H) 1.98 (d, J=5.86 Hz, 2H) 2.09-2.27 (m, 6H)2.34-2.50 (m, 2H) 3.39-3.49 (m, 1H) 3.53 (d, J=5.47 Hz, 2H) 3.64-3.81(m, 2H) 7.51 (d, J=8.21 Hz, 1H) 8.22 (d, J=8.21 Hz, 1H) 8.26 (s, 1H)8.45 (br. s., 1H)¹³C NMR (75 MHz, CHLOROFORM-d) δ ppm 13.38 (s, 1C)17.65 (s, 1C) 18.43 (s, 1C) 19.05 (s, 1C) 23.61 (s, 1C) 23.68 (s, 1C)23.78 (s, 1C) 23.99 (s, 1C) 36.68 (s, 1C) 50.06 (s, 1C) 66.17 (s, 1C)76.69 (s, 1C) 77.11 (s, 1C) 77.54 (s, 1C) 124.73 (s, 1C) 128.38 (s, 1C)129.42 (s, 1C) 133.08 (s, 1C) 144.51 (s, 1C) 150.43 (s, 1C) 164.33 (s,1C)³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 35.07 (s, 1P) C₂₅H₄₄N₂O₄P¹⁺ lowresolution ESI-MS calculated: 467.30, found: 467.31.

5′-DMTr-2′-TIPS-3′-(tributyl(3-(4-(1-hydroxypropan-2-yl)-3-nitrobenzamido)propyl)phosphoniumbromide)-uridine (59)

A two necked flask containing the triphosgene and phenanthridine wasconnected to a distillation head and condenser. The receiving end of thecondenser was attached to an ammonia trap and cooled by a dryice/acetone bath to condense the phosgene that was produced. The bottomof the ammonia trap was connected to a three necked round bottom flaskwith a stir bar which was also cooled by a dry ice/acetone bath. Allopen necks of round bottoms were sealed by fresh septa wrapped withTeflon tape. One neck of the three necked flask was punctured with a 20Gneedle attached to a tygon tube and two bubblers in series; the firstwas empty and the second contained mineral oil. Tygon tubing was used toconnect the second bubbler to a 9-inch 20G needle that was fullyinserted into a saturated solution of sodium hydroxide in methanol. Asecond needle and tube was inserted into the septa of the methanolicsodium hydroxide, which acted as a vent up into the fume hood.Triphosgene (1.87 g, 6.33 mmol) and cat. phenanthridine were heated to90° C., at which point the triphosgene melted and solvated thephenanthridine catalyst, promoting the evolution of phosgene gas. After30 min, all triphosgene was consumed and phosgene had begun condensingin the receiving flask. At this point a balloon of argon was puncturedthrough the septa on the two necked flask, pushing any phosgene gas tothe condenser and quenching solution. Once phosgene had stoppedcondensing, an acetonitrile solution of (57) (1.06 g, 1.9 mmol) wasadded dropwise to the stirring phosgene, then removed from the dryice/acetone bath after 10 min. The reaction was stirred for 2 h at roomtemperature. Next, argon gas was passed over the whole apparatus andalso bubbled through the reaction mixture into the methanolic sodiumhydroxide to remove and quench the excess phosgene. NOTE: a very lowflow from a balloon was used at first to ensure the phosgene wasquenched. Once all phosgene was removed, DIPEA (4 mL) was added to themixture to quench the HCl produced in the reaction with phosgene andcompound (57).

A solution of nucleoside (13) (1 eq, 1.35 g, 1.9 mmol) in ACN (3 mL) wasadded directly to the above mixture, and the resulting solution allowedto stir for 8 h at room temperature. The solution was diluted with ethylacetate and extracted with sat. NaHCO₃ (×3) and once with brine. Themixture was precipitated in 300 mL of MTBE to remove excess nucleosideand DIPEA. The resulting precipitate was then purified by columnchromatography (DCM:MeOH 100:0→90:10) to afford 1.32 g of (59) (62%yield).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.82-1.16 (m, 34H) 1.34 (dd,J=6.89, 2.20 Hz, 3H) 1.38-1.63 (m, 15H) 2.05 (br. s., 2H) 2.11-2.31 (m,12H) 2.67 (br. s., 1H) 3.39-3.53 (m, 1H) 3.57-3.72 (m, 3H) 3.78 (s, 7H)4.08-4.38 (m, 2H) 4.59-4.69 (m, 1H) 5.16-5.33 (m, 2H) 5.63-5.76 (m, 1H)6.00 (dd, J=5.27, 2.05 Hz, 1H) 6.81 (dd, J=8.79, 1.47 Hz, 4H) 7.15 (d,J=8.79 Hz, 1H) 7.18-7.41 (m, 10H) 7.56 (d, J=7.91 Hz, 1H) 7.88 (dd,J=8.20, 1.76 Hz, 1H) 8.53 (d, J=7.91 Hz, 1H) 8.67 (t, J=8.94 Hz, 2H)9.64 (br. s., 1H) C₆₅H₉₂N₄O₁₃PSi¹⁺ low resolution ESI-MS calculated:1195.61, found: 1195.60.

Compound (59) (316 mg, 0.29 mmol) was treated with 10 mL of 3% TFA inDCM followed by 0.5 mL of triethylsilane. This mixture was allowed tostir for 10 min followed by 5 mL of MeOH to further quench the tritylcation. This mixture was then diluted with 20 mL of toluene andconcentrated to near dryness. The mixture was then taken up in acetoneand precipitated in MTBE, filtered and solvated in DCM then condensed todryness. The above process was repeated once more to ensure there was notritylated material. The mixture was then co-evaporated with toluene todry. To this mixture, 1.5 eq of DCI was added (52 mg, 0.44 mmol) and 1.5eq of phosphoramidite (39) (362 mg, 0.44 mmol) was added and finallysolvated with 3 mL of ACN. This mixture was allowed to stir for 4 huntil all starting material was consumed as monitored by MS. The mixturewas then treated with 1 mL of tert-butanol to react with any excessphosphoramidite. This mixture was directly precipitated in MTBE:hexanes(75:25) to remove all excess reagents. The precipitate was solvated inDCM and treated with 1 mL of tert-butylhydroperoxide in decane andallowed to stir for 20 min until all starting material was oxidised, asmonitored by MS. This mixture was then precipitated in MTBE producingcompound pure (60) in 91% yield.

³¹P NMR (81 MHz, CHLOROFORM-d) 8 ppm −0.93 (s, 1P) −0.90 (s, 1P) −0.36(s, 1P) −0.31 (s, 1P) 34.20 (s, 1P).

Compound (60) was treated with UVB for 20 min, solvated in wet ACNproducing pure compound (47) in 92% yield after purification by columnchromatography (0→75% ethyl aceateLhexanes).

¹H NMR (300 MHz, CHLOROFORM-d) δ ppm 0.09-0.15 (m, 6H) 0.87-1.20 (m,40H) 1.94-2.00 (m, 1H) 2.10-2.20 (m, 2H) 3.44 (br. s., 3H) 3.67-3.79 (m,12H) 4.04-4.23 (m, 5H) 4.28-4.35 (m, 2H) 4.38-4.48 (m, 2H) 4.81-4.90 (m,1H) 5.38 (d, J=8.21 Hz, 1H) 5.64 (d, J=8.20 Hz, 1H) 5.81-5.91 (m, 2H)6.90 (d, J=7.91 Hz, 5H) 7.24-7.37 (m, 9H) 7.41-7.52 (m, 4H) 7.71 (dd,J=8.20, 2.64 Hz, 1H) 9.62 (br. s., 1H).

³¹P NMR (81 MHz, CHLOROFORM-d) δ ppm 0.58 (s, 1P) 0.83 (s, 1P).

While the disclosure has been described in connection with specificembodiments thereof, it will be understood that it is capable of furthermodifications and this application is intended to cover any variations,uses, or adaptations of the disclosure following, in general, theprinciples of the disclosure and including such departures from thepresent disclosures as come within known or customary practice withinthe art to which the disclosure pertains and as may be applied to theessential features herein before set forth, and as follows in the scopeof the appended claims.

Unless defined otherwise or the context clearly dictates otherwise, alltechnical and scientific terms used herein have the same meaning ascommonly understood by one of ordinary skill in the art to which thisinvention belongs. It should be understood that any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the invention.

All documents and references cited herein are hereby incorporated byreference in their entireties.

What is claimed is:
 1. A compound of formula (II):

wherein: n is an integer from 1 to 19; R₁ is a protecting group; R₃ isselected from H, a protecting group,

and an ionic tag linker; R₅ is selected from H, and a protecting group;R_(p) is a protecting group; R is lower alkyl, or the N(R)₂ moiety is acyclic alkylamine or a substituted cyclic alkylamine, preferablymorpholine; and B is a nitrogen-containing base; wherein each B, R₁ andR_(p) may be the same or different from any other B, R₁ and R_(p),respectively.
 2. The compound of claim 1, wherein the ionic linkercomprises: a photolabile moiety, an ionic moiety and a linker, whereinthe photolabile moiety is a nitrobenzyl derivative, and wherein theionic tag linker has the structure of formula (P):

wherein X is N or O, and wherein C3′ is the terminal 3′-hydroxyl of anoligoribonucleotide or oligodeoxiribonucleotide.
 3. The compound ofclaim 1, wherein: R₃ is

R₅ is selected from DMTr or MMTr; R_(p) is selected from methyl (Me),2-cyanoethyl (CNEt), ortho-chlorophenyl (o-ClPh), and para-chlorophenyl(p-ClPh); R is selected from isopropyl, methyl, and ethyl; and B is anucleobase protected on at least one nitrogen by a suitable N-protectinggroup.
 4. The compound of claim 3, wherein the N-protecting group isselected from levulinyl, acetyl, difluoroacetyl, trifluoroacetyl,isobutyryl, benzoyl, 9-fluorenylmethoxycarbonyl, phenoxyacetyl,dimethylformamidine, N,N-diphenyl carbamate and an ionic tag linker. 5.The compound of claim 1, wherein R₃ is

or a protecting group.
 6. The compound of claim 1, wherein theprotecting group is a levulinyl group (Lev) or an ionic tag linker. 7.The compound of claim 6, wherein the ionic tag linker comprises: aphotolabile moiety, an ionic moiety and a linker, wherein thephotolabile moiety is a nitrobenzyl derivative, and wherein the ionictag linker has the structure of formula (P):

wherein X is N or O, and wherein C3′ is the terminal 3′-hydroxyl of anoligoribonucleotide or oligodeoxiribonucleotide.
 8. A process forpreparing the compound of claim 1, wherein the compound has thestructure:

wherein: n is selected from 1, 2, and 3; R₁ is a protecting group; R₃ isselected from H, a protecting group and an ionic tag linker; R₅ is aprotecting group; R_(p) is a protecting group; and B is anitrogen-containing base; wherein each B, R₁ and R_(p) may be the sameor different from any other B, R₁ and R_(p), respectively; the processcomprising the steps of: (a) condensing a phosphoramidite of formula(III):

wherein B, R₁, R₅, and R_(p) are as defined above; and R is lower alkyl,or the N(R)₂ moiety is a cyclic alkylamine, or a substituted cyclicalkylamine, preferably morpholine; with a nucleoside of formula (IV):

wherein B and R₃ are as defined above; and (b) oxidizing the product ofstep (a) to produce the compound of formula (II) where n is 1, and B,R₁, R₃, R₅, and R_(p) are as defined above; and (c) where n>1, theprocess further comprising: (i) deprotecting the terminal —OR₅ group ofthe product of the previous step to form a free 5′-OH group; (ii)condensing the product of step (i) with a phosphoramidite of formula(III), wherein B, R₁, R₅, R_(p) and R are as defined above, and each B,R₁, R₅, R_(p) and R may be the same or different from any other B, R₁,R₅, R_(p) and R, respectively; (iii) oxidizing the product of step (ii);and (iv) repeating steps (i)-(iii) n−2 times; to form the compound offormula (II).
 9. The process of claim 8, wherein R₃ is H.
 10. Theprocess of claim 8, wherein R₃ is a protecting group, the processfurther comprising: (d) removal of the R₃ protecting group.
 11. Theprocess of claim 10, wherein the protecting group is a levulinyl (Lev)group or an ionic linker.
 12. The process of claim 11, wherein the ionictag linker comprises: a photolabile moiety, an ionic moiety and alinker, wherein the photolabile moiety is a nitrobenzyl derivative, andwherein the ionic tag linker has the structure of formula (P):

wherein X is N or O, and wherein C3′ is the terminal 3′-hydroxyl of anoligoribonucleotide or oligodeoxiribonucleotide.
 13. The process ofclaim 8, further comprising phosphitylation of the product of steps (b)or (c) to form a compound of formula (IIa):

wherein n, B, R₁, R₅, R_(p) and R are as previously defined.
 14. Theprocess of claim 8, further comprising phosphitylation of the product ofstep (d) to form a compound of formula (IIa):

wherein n, B, R₁, R₅, R_(p) and R are as previously defined.
 15. Theprocess of claim 8, wherein: R₁ is TBDMS; R₅ is selected from DMTr andMMTr; R_(p) is selected from methyl (Me), 2-cyanoethyl (CNEt),ortho-chlorophenyl (o-ClPh), and para-chlorophenyl (p-ClPh); R isselected from isopropyl, methyl, and ethyl; and B is a nucleobaseprotected on at least one nitrogen by a suitable N-protecting group,wherein the N-protecting group is selected from levulinyl, acetyl,difluoroacetyl, trifluoroacetyl, isobutyryl, benzoyl,9-fluorenylmethoxycarbonyl, phenoxyacetyl, dimethylformamidine, andN,N-diphenyl carbamate.
 16. A method for synthesizing anoligoribonucleotide or an oligodeoxyribonucleotide, the methodcomprising: (a) attaching an ionic tag linker to a first ribonucleosideor deoxyribonucleoside at the terminal 3′-hydroxyl; (b) contacting thefirst ribonucleoside or deoxyribonucleoside with at least one furtherribonucleoside or deoxyribonucleoside at reaction conditions to providean oligoribonucleotide or a deoxyribonucleotide comprising from 2 to 30ribonucleosides or deoxyribonucleosides; and (c) cleaving the ionic taglinker from the oligoribonucleotide or oligodeoxyribonucleotide toprovide the free oligoribonucleotide or oligodeoxyribonucleotide. 17.The method of claim 16, further comprising a step of isolating theoligoribonucleotide or the oligodeoxyribonucleotide before cleaving theionic tag linker in step (c).
 18. The method of claim 16, wherein theionic tag linker comprises: a photolabile moiety, an ionic moiety and alinker, wherein the photolabile moiety is a nitrobenzyl derivative, andwherein the ionic tag linker has the structure of formula (P):

wherein X is N or O, and wherein C3′ is the terminal 3′-hydroxyl of anoligoribonucleotide or oligodeoxiribonucleotide.
 19. The method of claim16, wherein the oligoribonucleotide or the oligodeoxyribonucleotide isisolated by precipitation.
 20. The method of claim 19, wherein theprecipitation is based on the ionic properties of the ionic tag linker.